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Revision: 129809
Author: m.riester
Date: 2017-05-23T18:05:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/DESCRIPTION
Modified  /trunk/madman/Rpacks/PureCN/R/setMappingBiasVcf.R
Modified  /trunk/madman/Rpacks/PureCN/inst/unitTests/test_setMappingBiasVcf.R
Fixed newly (1.7.9) introduced critical bug in setMappingBiasVcf.
Revision: 129808
Author: l.gatto
Date: 2017-05-23T14:21:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/mzR/DESCRIPTION
Modified  /trunk/madman/Rpacks/mzR/NEWS
Modified  /trunk/madman/Rpacks/mzR/R/io.R
Modified  /trunk/madman/Rpacks/mzR/man/openMSfile.Rd
merge conflict

From: Laurent <lg390@cam.ac.uk>
Revision: 129806
Author: d.childs
Date: 2017-05-23T11:56:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/TPP/R/tpptrFitSplines.R
Allow empty vectors for factorH0 argument when spline fitting 
Revision: 129804
Author: d.childs
Date: 2017-05-23T08:30:05+00:00
Paths:
Modified  /trunk/madman/Rpacks/TPP/DESCRIPTION
Modified  /trunk/madman/Rpacks/TPP/NAMESPACE
Fix namespace issues.
Revision: 129802
Author: m.riester
Date: 2017-05-23T03:11:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/PureCN/DESCRIPTION
Modified  /trunk/madman/Rpacks/PureCN/NAMESPACE
Modified  /trunk/madman/Rpacks/PureCN/NEWS
Modified  /trunk/madman/Rpacks/PureCN/R/PureCN-internal.R
Modified  /trunk/madman/Rpacks/PureCN/R/calculateBamCoverageByInterval.R
Modified  /trunk/madman/Rpacks/PureCN/R/calculateGCContentByInterval.R
Modified  /trunk/madman/Rpacks/PureCN/R/calculateLogRatio.R
Modified  /trunk/madman/Rpacks/PureCN/R/correctCoverageBias.R
Modified  /trunk/madman/Rpacks/PureCN/R/createNormalDatabase.R
Modified  /trunk/madman/Rpacks/PureCN/R/filterTargets.R
Modified  /trunk/madman/Rpacks/PureCN/R/filterVcf.R
Modified  /trunk/madman/Rpacks/PureCN/R/getSex.R
Modified  /trunk/madman/Rpacks/PureCN/R/readCoverageFile.R
Modified  /trunk/madman/Rpacks/PureCN/R/runAbsoluteCN.R
Modified  /trunk/madman/Rpacks/PureCN/inst/extdata/Coverage.R
Modified  /trunk/madman/Rpacks/PureCN/inst/extdata/IntervalFile.R
Modified  /trunk/madman/Rpacks/PureCN/inst/extdata/NormalDB.R
Modified  /trunk/madman/Rpacks/PureCN/inst/extdata/PureCN.R
Modified  /trunk/madman/Rpacks/PureCN/inst/unitTests/test_calculateGCContentByInterval.R
Modified  /trunk/madman/Rpacks/PureCN/inst/unitTests/test_createNormalDatabase.R
Modified  /trunk/madman/Rpacks/PureCN/inst/unitTests/test_runAbsoluteCN.R
Modified  /trunk/madman/Rpacks/PureCN/man/calculateGCContentByInterval.Rd
Modified  /trunk/madman/Rpacks/PureCN/man/filterTargets.Rd
Modified  /trunk/madman/Rpacks/PureCN/vignettes/PureCN.Rnw
Modified  /trunk/madman/Rpacks/PureCN/vignettes/Quick.Rnw
Added prototype off-target read support.
Revision: 129801
Author: a.oles
Date: 2017-05-22T22:26:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocWorkflowTools/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocWorkflowTools/NAMESPACE
Modified  /trunk/madman/Rpacks/BiocWorkflowTools/R/uploadToOverleaf.R
Fixed and improved handling of files and directories exclusion
Revision: 129799
Author: m.dunning
Date: 2017-05-22T19:57:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/beadarray/DESCRIPTION
Modified  /trunk/madman/Rpacks/beadarray/R/beadLevelData_summarize.R
Modified  /trunk/madman/Rpacks/beadarray/R/methods-ExpressionSetIllumina.R
Modified  /trunk/madman/Rpacks/beadarray/R/readIllumina.R
Modified  /trunk/madman/Rpacks/beadarray/R/readSampleSheet.R
Fixes to accomodate Illumina's 12-digit naming scheme. Thanks to Simon Kalteis for the tip-off and fixes.
Revision: 129797
Author: a.oles
Date: 2017-05-22T15:39:51+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocWorkflowTools/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocWorkflowTools/NAMESPACE
Modified  /trunk/madman/Rpacks/BiocWorkflowTools/R/uploadToOverleaf.R
Fix git initialization and add some sanity checks; exclude pdf files matching tex sources
Revision: 129795
Author: j.hon
Date: 2017-05-22T14:13:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/pqsfinder/DESCRIPTION
Modified  /trunk/madman/Rpacks/pqsfinder/src/pqsfinder.cpp
Added  /trunk/madman/Rpacks/pqsfinder/tests
Added  /trunk/madman/Rpacks/pqsfinder/tests/testthat
Added  /trunk/madman/Rpacks/pqsfinder/tests/testthat.R
Fixed bug in edge mismatch support.
Revision: 129790
Author: a.lun
Date: 2017-05-22T09:55:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/scran/inst/NEWS.Rd
Modified  /trunk/madman/Rpacks/scran/tests/testthat/test-correlate.R
Updated NEWS, tests.
Revision: 129788
Author: a.lun
Date: 2017-05-22T09:54:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/scran/DESCRIPTION
Modified  /trunk/madman/Rpacks/scran/R/correlatePairs.R
Bug fix to correlatePairs.
Revision: 129787
Author: a.conesa
Date: 2017-05-22T07:30:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/maSigPro/DESCRIPTION
Modified  /trunk/madman/Rpacks/maSigPro/R/seeDS.R
Modified  /trunk/madman/Rpacks/maSigPro/man/seeDS.Rd
Modified  /trunk/madman/Rpacks/maSigPro/man/tableDS.Rd
1 Warning, 1 Error and 2 NOTEs in new Rd an R files.
Revision: 129783
Author: k.bemis
Date: 2017-05-21T01:13:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/matter/DESCRIPTION
Modified  /trunk/madman/Rpacks/matter/NAMESPACE
Modified  /trunk/madman/Rpacks/matter/NEWS
Modified  /trunk/madman/Rpacks/matter/R/matter.R
Modified  /trunk/madman/Rpacks/matter/R/matter_df.R
Modified  /trunk/madman/Rpacks/matter/R/matter_list.R
Modified  /trunk/madman/Rpacks/matter/R/matter_str.R
Modified  /trunk/madman/Rpacks/matter/R/utils.R
Modified  /trunk/madman/Rpacks/matter/TODO
Modified  /trunk/madman/Rpacks/matter/data/matter_ex.rda
Added  /trunk/madman/Rpacks/matter/data/matter_msi.rda
Added  /trunk/madman/Rpacks/matter/data/matter_sim.rda
Deleted  /trunk/madman/Rpacks/matter/inst/vignettesExtra/matter-extra.Rnw
Deleted  /trunk/madman/Rpacks/matter/inst/vignettesExtra/matter-extra.bib
Modified  /trunk/madman/Rpacks/matter/man/bigglm.Rd
Modified  /trunk/madman/Rpacks/matter/man/delayed-ops.rd
Modified  /trunk/madman/Rpacks/matter/man/matter-class.Rd
Added  /trunk/madman/Rpacks/matter/man/matter_arr-class.Rd
Added  /trunk/madman/Rpacks/matter/man/matter_df.Rd
Modified  /trunk/madman/Rpacks/matter/man/matter_ex.Rd
Added  /trunk/madman/Rpacks/matter/man/matter_list-class.Rd
Modified  /trunk/madman/Rpacks/matter/man/matter_mat-class.rd
Added  /trunk/madman/Rpacks/matter/man/matter_str.Rd
Modified  /trunk/madman/Rpacks/matter/man/matter_vec-class.rd
Added  /trunk/madman/Rpacks/matter/man/profmem.Rd
Modified  /trunk/madman/Rpacks/matter/src/matter.cpp
Modified  /trunk/madman/Rpacks/matter/tests/testthat/test-methods.R
Added  /trunk/madman/Rpacks/matter/vignettes/matter-extra-1-sim.Rnw
Added  /trunk/madman/Rpacks/matter/vignettes/matter-extra-2-msi.Rnw
Modified  /trunk/madman/Rpacks/matter/vignettes/matter.Rnw
Modified  /trunk/madman/Rpacks/matter/vignettes/matter.bib
Added  /trunk/madman/Rpacks/matter/vignettes/msi-img.pdf
Added  /trunk/madman/Rpacks/matter/vignettes/msi-pc1.pdf
Added  /trunk/madman/Rpacks/matter/vignettes/msi-pc2.pdf
updated vignettes
Revision: 129782
Author: k.bemis
Date: 2017-05-21T01:13:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/matter/NAMESPACE
Modified  /trunk/madman/Rpacks/matter/R/prcomp.R
Modified  /trunk/madman/Rpacks/matter/src/matter.cpp
Modified  /trunk/madman/Rpacks/matter/tests/testthat/test-matter.R
Modified  /trunk/madman/Rpacks/matter/tests/testthat/test-methods.R
fixed bug in matrix mult
Revision: 129776
Author: j.gehring
Date: 2017-05-20T18:09:00+00:00
Paths:
Modified  /trunk/madman/Rpacks/SomaticSignatures/DESCRIPTION
Resolve incorrect loading of NMF namespace

Revision: 129772
Author: hpages
Date: 2017-05-20T00:59:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/HDF5Array/DESCRIPTION
Modified  /trunk/madman/Rpacks/HDF5Array/man/dump-management.Rd
add link to type() (documented in DelayedArray)
Revision: 129771
Author: hpages
Date: 2017-05-20T00:56:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/DelayedArray/DESCRIPTION
Modified  /trunk/madman/Rpacks/DelayedArray/man/DelayedArray-class.Rd
document type()
Revision: 129770
Author: hpages
Date: 2017-05-20T00:43:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/HDF5Array/man/dump-management.Rd
fix 2 typos
Revision: 129769
Author: hpages
Date: 2017-05-20T00:36:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/HDF5Array/NAMESPACE
Modified  /trunk/madman/Rpacks/HDF5Array/man/dump-management.Rd
export and document set/getHDF5DumpDir()
Revision: 129768
Author: hpages
Date: 2017-05-20T00:09:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/HDF5Array/man/dump-management.Rd
minor edit
Revision: 129767
Author: hpages
Date: 2017-05-20T00:06:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/HDF5Array/NAMESPACE
Modified  /trunk/madman/Rpacks/HDF5Array/R/dump-management.R
Modified  /trunk/madman/Rpacks/HDF5Array/R/writeHDF5Array.R
Modified  /trunk/madman/Rpacks/HDF5Array/man/dump-management.Rd
rename appendDatasetCreationToDumpLog -> appendDatasetCreationToHDF5DumpLog
Revision: 129766
Author: hpages
Date: 2017-05-19T23:40:21+00:00
Paths:
Modified  /trunk/madman/Rpacks/HDF5Array/DESCRIPTION
Modified  /trunk/madman/Rpacks/HDF5Array/NAMESPACE
Modified  /trunk/madman/Rpacks/HDF5Array/R/dump-management.R
Modified  /trunk/madman/Rpacks/HDF5Array/R/writeHDF5Array.R
Modified  /trunk/madman/Rpacks/HDF5Array/man/dump-management.Rd
Rename internal helper append_dataset_creation_to_dump_log() ->
appendDatasetCreationToDumpLog() and export and document it.
Revision: 129765
Author: l.gatto
Date: 2017-05-19T23:39:28+00:00
Paths:
Modified  /trunk/madman/Rpacks/pRolocGUI/R/pRolocVis.R
mention other dim reduction methods in pRolocVis man

From: Laurent <lg390@cam.ac.uk>
Revision: 129764
Author: l.gatto
Date: 2017-05-19T23:39:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/pRolocGUI/DESCRIPTION
Modified  /trunk/madman/Rpacks/pRolocGUI/NEWS.md
bump version

From: Laurent <lg390@cam.ac.uk>
Revision: 129763
Author: l.gatto
Date: 2017-05-19T23:39:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/pRolocGUI/R/pRolocVis_pca.R
assure that method is not matched multiple time to be able to use other dim red methods

From: Laurent <lg390@cam.ac.uk>
Revision: 129762
Author: l.gatto
Date: 2017-05-19T23:39:04+00:00
Paths:
Modified  /trunk/madman/Rpacks/pRolocGUI/R/pRolocVis_pca.R
avoids recomputing PCA at every reactive event

From: Laurent <lg390@cam.ac.uk>
Revision: 129761
Author: l.gatto
Date: 2017-05-19T23:38:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/pRolocGUI/R/pRolocVis_pca.R
fix issue #91

From: Laurent <lg390@cam.ac.uk>
Revision: 129759
Author: c.warden
Date: 2017-05-19T18:48:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/COHCAP/CHANGES
Modified  /trunk/madman/Rpacks/COHCAP/DESCRIPTION
Modified  /trunk/madman/Rpacks/COHCAP/R/COHCAP.integrate.avg.by.island.R
Modified  /trunk/madman/Rpacks/COHCAP/R/COHCAP.site.R
integration fixes
Revision: 129758
Author: mtmorgan
Date: 2017-05-19T17:33:18+00:00
Paths:
Added  /trunk/madman/Rpacks/IntramiRExploreR
Added  /trunk/madman/Rpacks/IntramiRExploreR/.travis.yml
Added  /trunk/madman/Rpacks/IntramiRExploreR/DESCRIPTION
Added  /trunk/madman/Rpacks/IntramiRExploreR/IntramiRExploreR.Rproj
Added  /trunk/madman/Rpacks/IntramiRExploreR/NAMESPACE
Added  /trunk/madman/Rpacks/IntramiRExploreR/News.md
Added  /trunk/madman/Rpacks/IntramiRExploreR/R
Added  /trunk/madman/Rpacks/IntramiRExploreR/R/Gene_Visualisation.r
Added  /trunk/madman/Rpacks/IntramiRExploreR/R/GetGOS_ALL.r
Added  /trunk/madman/Rpacks/IntramiRExploreR/R/IntraMirExploreR.r
Added  /trunk/madman/Rpacks/IntramiRExploreR/R/Visualisation.r
Added  /trunk/madman/Rpacks/IntramiRExploreR/R/data.r
Added  /trunk/madman/Rpacks/IntramiRExploreR/R/extract_miRNA_HostGene.r
Added  /trunk/madman/Rpacks/IntramiRExploreR/R/genes_Stat.r
Added  /trunk/madman/Rpacks/IntramiRExploreR/R/miRTargets_Stat.r
Added  /trunk/madman/Rpacks/IntramiRExploreR/README.md
Added  /trunk/madman/Rpacks/IntramiRExploreR/data
Added  /trunk/madman/Rpacks/IntramiRExploreR/data/Affy1_Distance_Final.RData
Added  /trunk/madman/Rpacks/IntramiRExploreR/data/Affy1_Pearson_Final.RData
Added  /trunk/madman/Rpacks/IntramiRExploreR/data/Affy2_Distance_Final.RData
Added  /trunk/madman/Rpacks/IntramiRExploreR/data/Affy2_Pearson_Final.RData
Added  /trunk/madman/Rpacks/IntramiRExploreR/data/miRNA_ID_to_Function.RData
Added  /trunk/madman/Rpacks/IntramiRExploreR/data/miRNA_summary_DB.RData
Added  /trunk/madman/Rpacks/IntramiRExploreR/inst
Added  /trunk/madman/Rpacks/IntramiRExploreR/man
Added  /trunk/madman/Rpacks/IntramiRExploreR/man/Affy1_Distance_Final.Rd
Added  /trunk/madman/Rpacks/IntramiRExploreR/man/Affy1_Pearson_Final.Rd
Added  /trunk/madman/Rpacks/IntramiRExploreR/man/Affy2_Distance_Final.Rd
Added  /trunk/madman/Rpacks/IntramiRExploreR/man/Affy2_Pearson_Final.Rd
Added  /trunk/madman/Rpacks/IntramiRExploreR/man/Gene_Visualisation.Rd
Added  /trunk/madman/Rpacks/IntramiRExploreR/man/GetGOS_ALL.Rd
Added  /trunk/madman/Rpacks/IntramiRExploreR/man/IntramiRExploreR.Rd
Added  /trunk/madman/Rpacks/IntramiRExploreR/man/Visualisation.Rd
Added  /trunk/madman/Rpacks/IntramiRExploreR/man/extract_HostGene.Rd
Added  /trunk/madman/Rpacks/IntramiRExploreR/man/extract_intragenic_miR.Rd
Added  /trunk/madman/Rpacks/IntramiRExploreR/man/genes_Stat.Rd
Added  /trunk/madman/Rpacks/IntramiRExploreR/man/miRNA_ID_to_Function.Rd
Added  /trunk/madman/Rpacks/IntramiRExploreR/man/miRNA_summary_DB.Rd
Added  /trunk/madman/Rpacks/IntramiRExploreR/man/miRTargets_Stat.Rd
Added  /trunk/madman/Rpacks/IntramiRExploreR/tests
Added  /trunk/madman/Rpacks/IntramiRExploreR/tests/testthat
Added  /trunk/madman/Rpacks/IntramiRExploreR/tests/testthat/test_ExtracthostGeneIntragenic.r
Added  /trunk/madman/Rpacks/IntramiRExploreR/tests/testthat/test_GetGOsALL.r
Added  /trunk/madman/Rpacks/IntramiRExploreR/tests/testthat/test_miRNAStat_geneStat.r
Added  /trunk/madman/Rpacks/IntramiRExploreR/tests/testthat.R
Added  /trunk/madman/Rpacks/IntramiRExploreR/vignettes
Added  /trunk/madman/Rpacks/IntramiRExploreR/vignettes/IntramiRExploreR_vignettes.Rmd
Modified  /trunk/madman/Rpacks/bioc_3.6.manifest
Added  /trunk/madman/Rpacks/ndexr
Added  /trunk/madman/Rpacks/ndexr/.Rbuildignore
Added  /trunk/madman/Rpacks/ndexr/DESCRIPTION
Added  /trunk/madman/Rpacks/ndexr/NAMESPACE
Added  /trunk/madman/Rpacks/ndexr/NEWS
Added  /trunk/madman/Rpacks/ndexr/R
Added  /trunk/madman/Rpacks/ndexr/R/ndex.R
Added  /trunk/madman/Rpacks/ndexr/R/ndex_RCX.r
Added  /trunk/madman/Rpacks/ndexr/R/ndex_api_config.r
Added  /trunk/madman/Rpacks/ndexr/R/ndex_api_config.yml
Added  /trunk/madman/Rpacks/ndexr/R/ndex_connect.r
Added  /trunk/madman/Rpacks/ndexr/R/ndex_groups.R
Added  /trunk/madman/Rpacks/ndexr/R/ndex_helper.r
Added  /trunk/madman/Rpacks/ndexr/R/ndex_networks.r
Added  /trunk/madman/Rpacks/ndexr/R/ndex_networks_aspects_and_metadata.r
Added  /trunk/madman/Rpacks/ndexr/R/ndex_networks_ndex_properties.r
Added  /trunk/madman/Rpacks/ndexr/R/ndex_networks_provenance.R
Added  /trunk/madman/Rpacks/ndexr/R/ndex_networks_simple_operations.r
Added  /trunk/madman/Rpacks/ndexr/R/ndex_ngraph.r
Added  /trunk/madman/Rpacks/ndexr/R/ndex_users.R
Added  /trunk/madman/Rpacks/ndexr/R/package_maintenance.R
Added  /trunk/madman/Rpacks/ndexr/README.md
Added  /trunk/madman/Rpacks/ndexr/man
Added  /trunk/madman/Rpacks/ndexr/man/listToRCode.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_conf_header.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_config.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_connect.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_create_group.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_create_network.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_create_user.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_delete_group.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_delete_network.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_delete_user.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_find_groups.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_find_networks.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_find_user_byId.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_find_user_byName.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_find_users.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_get_group.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_get_network.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_group_delete_membership.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_group_list_networks.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_group_list_users.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_group_network_get_permission.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_group_set_membership.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_helper_encodeParams.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_helper_getApi.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_helper_httpResponseHandler.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_internal_addAspects.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_network_aspect_get_metadata.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_network_delete_permission.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_network_get_aspect.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_network_get_metadata.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_network_get_permission.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_network_get_provenance.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_network_get_summary.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_network_set_systemProperties.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_network_update_aspect.Rd
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Added  /trunk/madman/Rpacks/ndexr/man/ndex_rest_DELETE.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_rest_GET.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_rest_POST.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_rest_PUT.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_update_group.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_update_network.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_update_user.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_user_change_password.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_user_forgot_password.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_user_get_networksummary.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_user_get_showcase.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_user_list_groups.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_user_list_permissions.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_user_mail_password.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_user_show_group.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_user_show_permission.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndex_verify_user.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ndexr-package.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ngraph_fromRCX.Rd
Added  /trunk/madman/Rpacks/ndexr/man/ngraph_toRCX.Rd
Added  /trunk/madman/Rpacks/ndexr/man/print.NDExConnection.Rd
Added  /trunk/madman/Rpacks/ndexr/man/print.RCX.Rd
Added  /trunk/madman/Rpacks/ndexr/man/rcx_asNewNetwork.Rd
Added  /trunk/madman/Rpacks/ndexr/man/rcx_aspect_toJSON.Rd
Added  /trunk/madman/Rpacks/ndexr/man/rcx_fromJSON.Rd
Added  /trunk/madman/Rpacks/ndexr/man/rcx_new.Rd
Added  /trunk/madman/Rpacks/ndexr/man/rcx_toJSON.Rd
Added  /trunk/madman/Rpacks/ndexr/man/rcx_toNGraph.Rd
Added  /trunk/madman/Rpacks/ndexr/man/rcx_updateMetaData.Rd
Added  /trunk/madman/Rpacks/ndexr/ndexr.Rproj
Added  /trunk/madman/Rpacks/ndexr/tests
Added  /trunk/madman/Rpacks/ndexr/tests/testthat
Added  /trunk/madman/Rpacks/ndexr/tests/testthat/helper_ndex_user.r
Added  /trunk/madman/Rpacks/ndexr/tests/testthat/helper_own_expect_functions.r
Added  /trunk/madman/Rpacks/ndexr/tests/testthat/test_00_helper_functions.r
Added  /trunk/madman/Rpacks/ndexr/tests/testthat/test_01_server_connection.r
Added  /trunk/madman/Rpacks/ndexr/tests/testthat/test_02_finding_networks.r
Added  /trunk/madman/Rpacks/ndexr/tests/testthat/test_03_simple_network_operations.r
Added  /trunk/madman/Rpacks/ndexr/tests/testthat/test_04_network_aspects_and_metadata.r
Added  /trunk/madman/Rpacks/ndexr/tests/testthat/test_05_rcx_model.r
Added  /trunk/madman/Rpacks/ndexr/tests/testthat/test_06_ndex_properties.r
Added  /trunk/madman/Rpacks/ndexr/tests/testthat/test_07_users.r
Added  /trunk/madman/Rpacks/ndexr/tests/testthat/test_08_groups.r
Added  /trunk/madman/Rpacks/ndexr/tests/testthat.R
Added  /trunk/madman/Rpacks/ndexr/tests_local.R
Added  /trunk/madman/Rpacks/ndexr/vignettes
Added  /trunk/madman/Rpacks/ndexr/vignettes/ndexr-vignette.Rmd
Adding ndexr, IntramiRExploreR
Revision: 129757
Author: j.rainer
Date: 2017-05-19T16:47:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/ensembldb/DESCRIPTION
Modified  /trunk/madman/Rpacks/ensembldb/R/Methods.R
Modified  /trunk/madman/Rpacks/ensembldb/R/dbhelpers.R
Modified  /trunk/madman/Rpacks/ensembldb/R/functions-create-EnsDb.R
Modified  /trunk/madman/Rpacks/ensembldb/R/functions-utils.R
Modified  /trunk/madman/Rpacks/ensembldb/inst/perl/get_gene_transcript_exon_tables.pl
Added  /trunk/madman/Rpacks/ensembldb/inst/scripts/checkEnsDbs.R
Modified  /trunk/madman/Rpacks/ensembldb/inst/scripts/generate-EnsDBs.R
Modified  /trunk/madman/Rpacks/ensembldb/man/EnsDb-AnnotationDbi.Rd
Modified  /trunk/madman/Rpacks/ensembldb/man/EnsDb-exonsBy.Rd
Modified  /trunk/madman/Rpacks/ensembldb/tests/testthat/test_Methods-Filter.R
Modified  /trunk/madman/Rpacks/ensembldb/tests/testthat/test_Methods.R
Modified  /trunk/madman/Rpacks/ensembldb/tests/testthat/test_functions-Filter.R
Modified  /trunk/madman/Rpacks/ensembldb/vignettes/ensembldb.Rmd
Modified  /trunk/madman/Rpacks/ensembldb/vignettes/ensembldb.org
Modified  /trunk/madman/Rpacks/ensembldb/vignettes/images/dblayout.png
Squashed commit of the following:

commit c5c099e9b13b5f1a9011aed07a3fe0a5fe51a46c
Merge: ee29c2f 2167c4d
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri May 19 18:44:16 2017 +0200

    Merge branch 'entrezid_table'

commit 2167c4d6968f18efb69e8acb4f7d397578f72648
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri May 19 07:43:40 2017 +0200

    Passes all tests for DBSCHEMAVERSION 2.0 (and 1.0)

    - Fixes issue #48.

commit ee29c2f6d4547009c8b817c50a88bfb890af404f
Merge: 5b20ac9 3602b9d
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu May 18 12:25:44 2017 +0200

    Merge branch 'devel'

commit 5b20ac9720a0408ab5401a11831e526ea7eea2e1
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu May 18 12:22:49 2017 +0200

    Disable code block execution in proteins.Rmd

commit 4c77cd72d7a4d25564088deb1045d02dd8a7e601
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu May 18 12:18:43 2017 +0200

    Test select and mapIds functions

    - Test select and malIds functions - seem to work.
    - Update documentation and vignette.

commit a184217f560402859c9429c872f0711ebf2a4b61
Merge: bb9295b 618b828
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed May 17 13:46:27 2017 +0200

    Merge branch 'master' into entrezid_table

commit bb9295b0582ea758c99c87fe386a9337e5b4fecf
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed May 17 13:03:57 2017 +0200

    Fix queries and results for all core API calls (issue #48)

    + Fix queries and results for genes, transcripts, exons etc calls.
    + Update documentation.

commit 9a14c0fc57dc3b2e43887f611a226223ce9524f2
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue May 16 21:06:21 2017 +0200

    Make validity method aware of different db schema versions

    - DB schema version dependent validity check.
    - DB schema version dependent index generation and database table creation (from
      Ensembl txt files).

commit 618b8283e089ef359c2aba1544f20801114fcc3d
Merge: 60f1609 428714c
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue May 16 19:20:16 2017 +0200

    Merge branch 'devel'

commit 60f1609fe58cff8c8437d419b461d66678b05f16
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue May 16 17:28:38 2017 +0200

    Fix problem if multiple non-unique values passed to a filter

    - Enable proteins vignette.

commit dd0ee243bd80c907f6bdc476cc3a7080b1da3d09
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue May 16 17:13:10 2017 +0200

    Modify perl script to save entrezid in separate table

commit 1998c53bac866f00b87a30099746575a1edc72a7
Merge: 48473d2 1a7f0ea
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon May 8 09:47:30 2017 +0200

    Merge branch 'devel'

commit 48473d2cfefdb249de54a266ae82be439f515598
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon May 8 09:40:35 2017 +0200

    Tentative fix for TIMEOUT errors (issue #47)

    - Delete MySQL-backend.Rmd, proteins.Rmd.
    - Disable all code chunks requiring network access.

commit 3090d70cda67c5c5bcc59183533a780084a3b031
Merge: 50d3eb3 79cb29d
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Sat May 6 22:08:34 2017 +0200

    Merge branch 'devel'

commit 50d3eb30e5a396b74d02ac910cfc501798a31d1c
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Sat May 6 19:23:14 2017 +0200

    Disable all proteins.Rmd chunks

    This is to evaluate what causes the TIMEOUT error on Windows.

commit 5db914e91d30c7b2a3b92c430dd94efd14d5b977
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Apr 28 11:09:13 2017 +0200

    Use curl instead of Rcurl package

commit 663888158882e924aaea721a4ec72d72efb307ef
Merge: 1faf673 8368588
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Apr 28 10:29:45 2017 +0200

    Merge branch 'devel'

commit 1faf6734e63c61e6f78ada1daad53378c0c15b28
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Apr 28 10:16:00 2017 +0200

    Add ggbio and Gviz to suggested packages.

commit 4a7bb3727c0ffcaa58b38721fcde784b85de3238
Merge: fc85c0f 7828612
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Apr 28 10:03:26 2017 +0200

    Merge branch 'devel'

commit fc85c0f3465e30f474b820b965eec7d48acfcdb5
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Apr 28 10:01:34 2017 +0200

    Add ggbio and Gviz as required packages for the vignette

commit ffd5c090c6c4438ded1037f713e45e5e5e13a9ea
Merge: f9616c8 5bb7f2e
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Apr 7 10:30:51 2017 +0200

    Merge branch 'devel'

commit f9616c84da147c2de0c67f59498892ea0bfd41bd
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Apr 7 10:26:12 2017 +0200

    Enable Gviz plotting again in vignette

    - Enable the Gviz plotting examples again in the vignette.
    - Add an example for ggbio to the vignette.

commit dae7fa9743429983b56ef1221a786f574b08387b
Merge: 8a308eb c672d54
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Apr 3 08:46:22 2017 +0200

    Merge branch 'devel'

commit 8a308eb63dd691f47f1bccc1de35b15ca19e3724
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Apr 3 08:22:10 2017 +0200

    Update readme.md

commit 1109c5cd5ad0823b07d8a7a8dd3e236633530981
Merge: c82d2cc 870dc38
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Apr 3 08:20:30 2017 +0200

    Merge branch 'AnnotationFilters'

commit 870dc38be532528dd984d6cf0c7f82c0db90fe6d
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Mar 31 06:00:30 2017 +0200

    Add fetching from AnnotationHub to the vignette

commit f40e11772b82fddf0a1c52faf41d5513e5ef92a6
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Mar 29 14:33:53 2017 +0200

    Add BiocSticker to readme.org

commit fb9078c1314183c01714205ba792b165bd6406b6
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Mar 29 09:25:02 2017 +0200

    Remove debug messages

commit fd1416c3e57a2c614f5467aaea816cae1ae68b8e
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Mar 28 11:00:40 2017 +0200

    Disable Gviz to fix transition phase

commit 425f358926bc3f720d59c07a171ad231e67c7f22
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Mar 27 09:38:21 2017 +0200

    Fix documentation and examples

commit 1b33de9b6add5a18d96203bf8384234236912469
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Mar 27 08:02:03 2017 +0200

    Fix all unit tests

    o Switch from RUnit to testthat and update/fix all unit tests.

commit a0e2adce7cc4357968376d72eaf180d87dc23917
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Mar 22 11:10:12 2017 +0100

    Add ensDbQuery,AnnotationFilterList method (issue #42)

    - Add the internal ensDbQuery,AnnotationFilterList method (issue #42).
    - Add related unit tests.

commit 2a01008b86aeb2f03004353bab40c3f40259a995
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Mar 22 06:56:14 2017 +0100

    Support the GRangesFilter from AnnotationFilter (issue #44)

    - Add support for the GRangesFilter from AnnotationFilter.
    - Add related documentation and unit tests.

commit 7a114b51ee32f7dd75f303286fbf7ac1cd8250ac
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Mar 21 16:56:34 2017 +0100

    Add .processFilterParam function (issue #41)

commit c82d2cc0d80c85adcd7a008b3d24336d5ca1f506
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Sun Mar 5 19:38:28 2017 +0100

    Remove readme.org and update readme.md

commit 31f46018050956bdcf8d1522ee533d26da59b27d
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Sun Mar 5 19:34:21 2017 +0100

    Add readme.md

commit 54feb88954392159e6c7b4b9ab8b0da9f6b503c0
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Sun Mar 5 19:20:01 2017 +0100

    Add ensembldb sticker to readme

commit eaecfd9b49dab1545eeafaed6b712e700248c614
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Sun Mar 5 19:16:53 2017 +0100

    Switch to AnnotationFilter

commit 933cdd837bf2682c997a071237eb7f832090b185
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Feb 9 12:07:30 2017 +0100

    Import AnnotationFilter classes from AnnotationFilters

    o Replace internal filters by AnnotationFilters.
    o Remove obsolete methods where, column etc.
    o Add ensDbColumn and ensDbQuery to replace the above functionality.

commit 07d6540df4983de6d3ccf4347a2b1ea8b3ce2ef8
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Sun Feb 5 15:55:57 2017 +0100

    Some notes on Organism.dplyr

commit fc3f870c610f3f1dabdccf76568e6a71ee6f82e0
Merge: a6982a5 d601c64
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Jan 26 09:49:31 2017 +0100

    Merge branch 'devel'

commit a6982a5b5137a9c8bbe56dec63056b865029b54c
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Jan 26 09:44:31 2017 +0100

    Fix problem fetching sequence lengths from ensemblgenomes, issue #32

commit a62c2d85e03f8eada285dc2bbd8b88a119ce5103
Merge: 7cb3246 fb1bdc1
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Sat Jan 14 21:13:00 2017 +0100

    Merge branch 'devel'

commit 7cb3246f36d983acadd79e5628c7027ac3adaa46
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Sat Jan 14 19:22:32 2017 +0100

    Extract also taxonomy ID from the Ensembl databases

    o Extract the species' taxonomy ID from the Ensembl database and store it to the
      metadata table.

commit 4f3e1a49ec23f3cacb7711ee35f8d7a252f51c4c
Merge: c8fd410 2be5cb2
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Jan 10 13:30:22 2017 +0100

    Merge branch 'devel'

commit c8fd410086370c20d00e329c24745446fde3cc34
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Jan 10 13:18:04 2017 +0100

    Small change in the title

commit b36660c9d246dd3f5a3b88f1957dc4274b2145c1
Merge: 78af2fa 2871396
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Dec 20 09:28:39 2016 +0100

    Merge branch 'devel'

commit 78af2fa1230cb969dafed38546ad678b3c958817
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Dec 20 09:17:05 2016 +0100

    Fix Windows check error (issue #25)

    o Fix the unit test error for retrieving mysql database files from Ensembl in
      Windows.

commit b982e404de68b135cc66b4cd55c41081006d060a
Merge: f7c662a 9bc2afa
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Dec 15 19:30:11 2016 +0100

    Merge branch 'devel'

commit f7c662aedad9c0125aba48ff6c7dfef7930308e3
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Dec 15 19:21:09 2016 +0100

    Small documentation fix

commit a03830bf29249c540087bf1f04223f35a299f047
Merge: 959681d 3af77a2
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Dec 7 14:11:11 2016 +0100

    Merge branch 'devel'

commit 959681d36bcc163a07048dad9a7cb45544f95e2b
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Dec 7 12:59:38 2016 +0100

    Update to new BiocStyle vignettes.

commit c1843530866837ca6c0296418bda0adbee177f3d
Merge: 5b2ca8e 0672229
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Dec 1 11:14:59 2016 +0100

    Merge branch 'devel'

commit 5b2ca8e3b2610c2e15f6acb6fd5c073dc414e4e0
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Dec 1 10:49:26 2016 +0100

    Fix vignette problems.

commit 6471e50160aedb42af7b6e68b789bc5723725ec3
Merge: 7d88fd1 3d2ba33
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Nov 28 13:16:31 2016 +0100

    Merge branch 'devel'

commit 7d88fd126f502c86205bf2a4b1737c16f9012e03
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Nov 28 13:12:26 2016 +0100

    Fix MySQL backend related bugs.

    o Fix wrong database naming when inserting EnsDb built from GTF/GFF.
    o Avoid error for creating an MySQL index for a column without values.

commit 07bcb39fcb5b1a72e26aef0bd7aef5fdcd4e55dd
Merge: a794d58 c5b23c5
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Nov 23 14:51:10 2016 +0100

    Merge branch 'devel'

commit a794d58476f078c59053c480b710bd015b32b48b
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Nov 23 14:39:47 2016 +0100

    Export OnlyCodingTxFilter.

commit b2641aa5989ede4b14875240b14f580657d8b3a1
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Nov 22 12:44:03 2016 +0100

    Add a helper function to read species from ftp dir

    o Add a simple helper function to retrieve an array with the species from an ftp
      folder.

commit 1c10a930e98939c246c8c8a009066c394fd73b93
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Nov 21 06:50:08 2016 +0100

    Fix unit test error.

commit 8d04a6d0febbf195717bb489dd55adca4991c294
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Nov 17 07:49:47 2016 +0100

    Small fix in the scripts to create EnsDbs.

commit a2a0b7655b8e8e5fe2b08bf30297f553d4417680
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Nov 15 17:18:50 2016 +0100

    Add unit tests for Uniprot db and mapping type filters

commit 9d348d8a9fe585e6a1b8efed3a375c54d582e877
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Nov 15 07:52:13 2016 +0100

    Extend proteins vignette and fix createEnsDbs script.

commit 8af36db823698b0b4c55a7242937223f9832c5d3
Merge: dbc2acd 354d885
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Nov 14 19:20:39 2016 +0100

    Merge branch 'devel'

commit dbc2acd9a5b8ad2bca000afac5d8ebbcd8ff99e6
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Nov 14 19:16:21 2016 +0100

    Fix bug in example.

commit 6ecca8aea1505abe75487b7aa9822e45f08c38a5
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Nov 14 18:40:22 2016 +0100

    Update proteins vignette.

commit 50095736dd13bf59ae2db9a98c25b3e3e947f778
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Nov 14 16:24:36 2016 +0100

    Update Protein Filters documentation.

commit 0ef7be0a7e238bd45c4b5dceb45fee242bcec29b
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Nov 14 16:13:59 2016 +0100

    Add column and where methods for new filters

    o Add column and where methods for UniprotdbFilter and UniprotmappingtypeFilter.
    o Add unit tests for the new filters.
    o Adapt isProteinFilter for the new filters.

commit ec9e38f72c6cc2f47365b1dee30259bc8e88c425
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Nov 14 14:13:54 2016 +0100

    Fix return statements in server.R

commit 6a6325d00d0e474a36e0c1f9312798834d2b90a4
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Nov 14 09:30:49 2016 +0100

    Add filters for the new Uniprot database columns

    o Add UniprotdbFilter and UniprotmappingtypeFilter (issue #29).

commit de67102fb1a0f6857aa3913cd4faba98768f8a49
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Nov 14 06:34:23 2016 +0100

    Add a function to create EnsDb packages

    o Add a function to create EnsDb packages from SQLite database files found in
      the specified directory.

commit a5639cbdb9d3c274d7060375985da4fcf7164037
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Sun Nov 13 18:57:47 2016 +0100

    Add script to automatically generate EnsDbs from Ensembl

    o Add script with functions to fetch and install Ensembl databases locally and
      generate EnsDbs from them (issue #26).

commit 5d94515d945130dbe6ea5a31df57e3a3a3950ac5
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Sun Nov 13 18:48:31 2016 +0100

    Fetch Uniprot DB and mapping type

    o Fetch also the Uniprot database and the method type which was used to map the
      Uniprot ID to the Ensembl protein ID.

commit a9dd1ea3a15b6fb602dfe60e362724261a0a9e53
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Nov 11 12:46:11 2016 +0100

    Fix small problem in internal compareProteins function.

commit 14f4427cd73eedf53cf8d16edbc6a5eee261ea8f
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Nov 11 12:34:43 2016 +0100

    Fix error in perl script for database without genome

    o Transform sequence features always to "toplevel" instead of "chromosome" in
      the perl script. This avoids an error when "chromosome" is not available
      (e.g. for anas_platyrhynchus). (issue #27).

commit 6122699d6ae95ee0696dface05f8babd05d901e3
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Nov 9 16:16:21 2016 +0100

    Fix bug preventing index creation

    o Fix bug that prevented index creation on protein tables when inserting an
      EnsDb with protein data into MySQL.
    o Update org file to org-mode 9.0 syntax.

commit 7c6b6f5383c33e347d43cc4003914697a7835921
Merge: e9da2d8 554c650
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Oct 20 10:07:36 2016 +0200

    Merge branch 'devel'

commit e9da2d8be53d37aa6e0c8e0c01caca9c4fc93e9d
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Oct 20 08:10:43 2016 +0200

    Bump version to 1.99.0

commit a1b9b43cabd2c9b8812c1bc6c9e581c0d4dc932d
Merge: 503f695 753c2f9
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Oct 20 08:08:56 2016 +0200

    Merge branch 'proteins'

commit 503f695c1ba18c3a34ae475647e115f7404df63e
Merge: 6467b5e a582305
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Oct 20 08:06:39 2016 +0200

    Merge branch 'devel'

commit 753c2f901f944f0737131c82a33993283c285cbf
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Oct 14 15:12:17 2016 +0200

    Update the proteins vignette

commit 6f4d832a5ae9867da30db73f2b18ec3fd8942413
Merge: a83f522 6af572c
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Oct 14 14:27:15 2016 +0200

    Merge branch 'proteins' of https://github.com/jotsetung/ensembldb into proteins

commit a83f5223d1c66ec7cb91885cd0ba48f12431364f
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Oct 14 14:20:37 2016 +0200

    Add mapIds support for protein annotations.

    o Add unit tests ensuring that mapIds works with protein annotations.

commit 6af572c03f1772055e19d3cf6d4d83ce081fe385
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Oct 14 14:20:37 2016 +0200

    Add mapIds support for protein annotations.

    o Add unit tests ensuring that mapIds works with protein annotations.

commit 66ad37fb79eaea8367c4ed639601f3b261aa9b4c
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Oct 14 12:45:53 2016 +0200

    Add protein support for AnnotationDbi methods

    o keys, keytypes and select support now protein annotation columns and
      filters.
    o Add unit tests to validate that the data returned by select matches
      what is expected.

commit f389626ac0fa3e443dd92cded3f521865b5e7210
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Oct 12 08:12:39 2016 +0200

    Add internal compareProteins function

commit bd86300865940b7a486fd04bc1b6b23bd24e70fe
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Oct 12 06:49:01 2016 +0200

    Fix smaller issues from R CMD check

commit 03f5a295d2f2da71e9f557d3f041d89b03a32200
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Oct 11 22:26:20 2016 +0200

    Remove exon columns from proteins call

    o Remove exon specific columns in proteins method.
    o Fix unit test problem.
    o Update NEWS.

commit 7bd37e13f9114138940fdc6b35d8b90b4bfabf8f
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Oct 11 22:17:47 2016 +0200

    Implement utilities to fetch seqlengths

    o Implement utilities to fetch sequence lenghts from Ensembl or
      Ensemblgenomes replacing the ::: imports from GenomicFeatures.
    o Fix the proteins method returning now by default a DataFrame.
    o Add unit tests.

commit 4d488575387f07ff56fc5b8be9683e87ba6cfe7b
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Oct 5 14:45:45 2016 +0200

    Fix build and check errors

    o Fix the build and check errors if EnsDb.Hsapiens.v75 does not contain
      protein annotations.

commit 289f10eb19ca99459eb586a2a5ad07fe6ab43015
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Oct 5 12:29:15 2016 +0200

    Add proteins vignette

    o Add proteins vignette.
    o Add proteins method, documentation and unit tests.

commit c90a81e64e53d584fe90ecc3cf37f129431f84a3
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Oct 4 18:14:05 2016 +0200

    Add some more protein related unit tests

    o Add protein related unit tests.
    o Start implementing the proteins method.

commit c4606281b7838b93e4f6a3d23a2f8472d750f745
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Oct 4 15:25:40 2016 +0200

    Add extended EnsDb validity method

    o Check for correctness of database content (issue #19).

commit 5a862bc4698627463a80d1ef0d6d7e02f65db33a
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Oct 4 14:43:05 2016 +0200

    Fix unit test failure.

    o New query engine fixing issue #18.

commit 103b15a0fe8956133141105f0ce3f24ce34480a4
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Oct 4 14:06:05 2016 +0200

    Implement new query engine

    o New query engine uses "join" for all DNA/RNA tables and "left outer join"
      for joins within the protein space and between protein and RNA/DNA tables.
    o Selection of required tables for provided query names does now
      consider only the ordering of tables as returned by listTables. No
      more query optimization by reducing the numbers of tables to join.

commit af90f40223ea877a7d8972fb9f47d61164f7fbaa
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Oct 3 10:54:56 2016 +0200

    Some more unit tests

commit 964597d8080f2f2e13d0f59236ab45b505732d0c
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Oct 3 08:57:40 2016 +0200

    Fix accidental deletion of random lines

    o Add new database layout image.

commit bed7bb837eb3a543df01f2b4a8fb586e54137f1f
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Oct 3 08:24:53 2016 +0200

    Fix unit test failure

    o Fix unit test failure.
    o Add more unit tests.

commit 7aae6337c5aa509a437beb6fefba79e5f9c38d9c
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Sat Oct 1 20:05:55 2016 +0200

    Add more unit tests.

commit 608419c347e65cd937ff7d091f508dd126c3e824
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Sep 30 18:47:52 2016 +0200

    Add protein filter documentation

    o Add documentation for protein filters.
    o Add some more unit tests.
    o Create indices also for protein_domain_id and uniprot_id.

commit 4802498a8768bb0a56d128242101ec17d0659487
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Sep 30 11:26:57 2016 +0200

    Fix bug in perl script

    o Fix minor bug in perl script.
    o Add ProteinidFilter, UniprotidFilter and ProtdomidFilter classes along
      with required methods.
    o Add more unit tests.

commit b9b4c8b4e97c9f7fcae6d257833e3e329e3f56a8
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Sep 29 16:25:15 2016 +0200

    Code tidying and some more unit tests.

commit 72a5dd7bcdc301136e9a873befbde17a9662adc2
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Sep 29 15:28:55 2016 +0200

    Add some more unit tests.

commit a7187bc18abe5080166a50b8e63930fabb08eafd
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Sep 29 09:37:31 2016 +0200

    Support querying for protein annotation columns

    o Add support for protein annotation columns in the column parameter of
      data access methods.
    o Code tidying.
    o Increase the number of unit test to cover more functionality.

commit 455cdf7ee9e09befb8161a72acdcc784c974179b
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Sep 28 14:43:16 2016 +0200

    Start implementing base support for protein tables

    o Create required database tables and import them.
    o Add additional unit tests ensuring correct evaluation.
    o Restructure Generics.R

commit 696ef5c77ab86d76215b372909f386bd694eced6
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Sep 28 11:19:32 2016 +0200

    Fetch also peptide sequence from Ensembl.

commit 742fe4597078b806da6d5dee8746afc68fa4ce86
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Sep 28 06:47:56 2016 +0200

    Fetch protein features from Ensembl

    o Add functionality to the perl script to fetch protein data from
      Ensembl.
    o Add a proteins.org file/vignette.

commit 6467b5ee7362bb7b31a999881d14156edaa68598
Merge: 7fa1a80 deb8304
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Sep 20 22:14:04 2016 +0200

    Merge branch 'devel'

commit 7fa1a80fa0bd44c717ab31d5c821bebe2d753a7f
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Sep 20 15:31:07 2016 +0200

    Add some more MySQL stuff

    o Add listEnsDbs functions to list EnsDb databases in a MySQL server.
    o useMySQL compares dates/versions between package based and MySQL based
      databases (issue #16).
    o If a DBIConnection is provided, the EnsDb function allows to connect
      directly to a MySQL EnsDb database (issue #17).
    o Add vignette describing MySQL usage.

commit b02a4e8829727e3381440bf3a0a0e9e0728788f8
Merge: 06135d6 8f6b553
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Sep 16 14:09:06 2016 +0200

    Merge branch 'devel'

commit 06135d630880720e21d7320eb30ec776f2f16197
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Sep 16 13:53:06 2016 +0200

    Implement MySQL support.

    o Implement functions to save the EnsDb data into a MySQL database and
      switch from SQLite to MySQL backend (issue #12).

commit 6aa0e1abb478d515ab9638226f63322413183024
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Sep 16 13:06:22 2016 +0200

    Add useMySQL method to switch SQL backend

    o useMySQL saves all data into a MySQL database and uses this as
      backend.
    o Enhance the validity method on EnsDb.

commit 34565225388a8ff298da13e80abf13c305259060
Merge: 2756915 14a7281
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Sep 16 08:29:56 2016 +0200

    Merge branch 'devel'

commit 275691582048e73633326a12c50528b90ec9e22f
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Sep 15 16:22:23 2016 +0200

    Bump version and fix issue #11

    o Issue #11 will be fixed for newly generated databases as the new
      indices improve the performance. The sorting in R in cdsBy does
      not fix issue #11, but alleviates the performance loss.

commit f6dfe44883782ecfca89e3bd1907e9c3e69be9d7
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Sep 15 16:19:07 2016 +0200

    Check and fix ordering in all methods

    o Fix ordering in cdsBy, fiveUTRsByTranscript, etc.
    o Add an internal filter class that enables filtering on
      tx_cds_seq_start being NULL.

commit 7ca7d7e41ddf721f3c9792f8385649501ec808c0
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Sep 15 10:08:27 2016 +0200

    Add additional indices to new databases

    o Add additional indices to newly created databases which increases the
      performance considerably.

commit a97216dcca15af05be631e7a4bfc7229c16aca94
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Sep 15 08:55:39 2016 +0200

    Enable switching between R and SQL ordering

    o Add internal orderResultsInR method to enable switching between
      ordering of the results in R and SQL.
    o Fix ordering bug.

commit 9e952ef562474d859bd8b708536596ff917f8066
Merge: b8920cd 06cfa6d
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Sep 13 15:34:48 2016 +0200

    Merge branch 'devel'

commit b8920cdf310cf1aab05a3de93b246ba334116f06
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Sep 13 15:29:57 2016 +0200

    Enforce tx_cds_seq_start to be of type integer

    o Perform sanity checks on input tables/data in
      makeEnsemblSQLiteFromTables and ensDbFromGRanges.
    o Enforce tx_cds_seq_start and tx_cds_seq_end SQL database columns to be
      of type INTEGER.

commit 38a40101ad7f78c91f45aa1ab3364ee2e8983950
Merge: b144c1f 87ff129
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Aug 24 09:23:40 2016 +0200

    Merge branch 'devel'

commit b144c1f6f9ddd9b561737e6b5515281ff988ebee
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Aug 24 09:19:45 2016 +0200

    Change vignette style.

commit f1656ef10f93296ac67f677e6b2b6a96585f73f6
Merge: 50c89cf ea04b32
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Jul 1 07:41:36 2016 +0200

    Merge branch 'devel'

commit 50c89cf5c3caf59240ad8d95dd10789eedd258b6
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Jul 1 07:33:44 2016 +0200

    New SymbolFilter, SYMBOL support

    o New SymbolFilter.
    o Support for columns symbol and SYMBOL.
    o select method ensures ordering matches keys if keys is a character
      vector or a single filter.
    o Update of man pages and vignette.

commit 0c2b56b16eddb99f0b12c0c8cbd41db9f5bfca8d
Merge: 323e08c 0e2a378
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Jun 30 13:41:33 2016 +0200

    Merge branch 'devel'

commit 323e08c20e448b8b14ada9d4ccd8cc7f77b4e301
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Jun 30 13:35:10 2016 +0200

    New SymbolFilter and support for symbol column.

    o New SymbolFilter and support for a (virtual) columns symbol that
      symlinks to the gene_name database column.
    o returnFilterColumns method to enable/disable the option to return all
      columns required for specified filters in the output.
    o Support for SYMBOL column and keys in the select method.
    o Select method does ensure result ordering matches the input keys if a
      single filter or only keys are provided.

commit e2a0a288e41901665b39b1e910b255068d0d4be8
Merge: 23eb75a 7fd4140
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Jun 6 08:59:52 2016 +0200

    Merge branch 'devel'

commit 23eb75ac6217a7ca7f577d7d8d1a02b86d0b3492
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Jun 6 08:56:56 2016 +0200

    Fix bug in ensDbFromGRanges

    o Fix error in ensDbFromGRanges if organism is whitespace-separated.

commit ed0fb0503b184a8142cac1df7eefc599772cfb87
Merge: 66920ee 6f303a5
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Jun 1 11:02:19 2016 +0200

    Merge branch 'devel'

commit 66920ee113c3411d291d22dbaf44f88ada54ee6e
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Jun 1 10:42:53 2016 +0200

    Fix typos in documentation.

commit 5d9f1882352f15ac4d4e21dfd2241f4ff5186128
Merge: bcbc352 295961b
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue May 31 08:17:41 2016 +0200

    Merge branch 'devel'

commit bcbc3526172f15b2569d525dd7e50df3a11d2efb
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue May 31 08:14:18 2016 +0200

    Fix small bug in validation of BasicFilter.

commit 2966e6e182eb3e10390804b1230cb29753eb7987
Merge: 8115655 065d3dc
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed May 25 09:17:09 2016 +0200

    Merge branch 'devel'

commit 8115655779410c09214c67c0d519e1ae70099879
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed May 25 09:13:31 2016 +0200

    Fix another bug in exonsBy.

commit 342f631e143b2c739a0a47bf0df35c7d1aff60b4
Merge: da92adc 65178ec
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed May 25 08:42:47 2016 +0200

    Merge branch 'devel'

commit da92adcc3c0b6791a05b8152e6f27a0fc17926a8
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed May 25 07:17:35 2016 +0200

    Update NEWS and DESCRIPTION.

commit 4d34b925b565c91e69928f303301fab047eaabc8
Author: j.rainer <j.rainer@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date:   Tue May 24 19:44:38 2016 +0000

    Bug fixes

    o Column tx_id was always removed from exonsBy result even if in the
      columns argument.
    o exon_idx was of type character if database generated from a GTF file.

    From: jotsetung <johannes.rainer@gmail.com>

    git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/ensembldb@117813 bc3139a8-67e5-0310-9ffc-ced21a209358

commit c183486ab9881b6ac1a30bbab343286eb8c2d322
Merge: d909388 ad3c1af
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed May 4 12:27:13 2016 +0200

    Merge branch 'devel'

commit d9093883a0c0963c92680cf80dbc0ef5870b036b
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed May 4 11:57:48 2016 +0200

    Just add a new NEWS

commit d0def84c72fca960af3e3a7db9880a2ea7abd9c7
Merge: 3c11ac7 57b5d56
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed May 4 11:56:14 2016 +0200

    Merge branch 'devel'

commit 3c11ac7aeeb9c4247565255fa01ba72127dc5b20
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed May 4 10:17:45 2016 +0200

    Add support for column "tx_name"

    o "tx_name" can now be provided with the columns argument of all
      methods. The methods return the tx_id from the database.

commit d9d3fb4a4b317596bf9b0344895c584b07b0e26f
Merge: 7bb8084 b2ae6c5
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon May 2 10:18:06 2016 +0200

    Merge branch 'devel'

commit 7bb8084e7e239dae288426cf38423f24ce7f1cec
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon May 2 09:48:36 2016 +0200

    Fix bugs in transcripts, genes, exons etc methods

    o Fix a bug in transcript, genes etc methods that results in an error if
      with argument columns columns are specified which are not in the
      database.
    o Remove the transcriptLengths implementation in ensembldb; use the one
      from GenomicFeatures instead.

commit 70c177059485b25e8a04b47b887a32640787722b
Merge: 7d55363 839fc1b
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Apr 1 13:42:32 2016 +0200

    Merge branch 'devel'

commit 7d553636a07574efc7449373c89b7b8f912d2fb5
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Apr 1 13:38:36 2016 +0200

    Support Ensembl GTF files < 75.

commit 59f616bd3e9a78a833e276e0704a3fc5f43d4857
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Mar 9 16:02:21 2016 +0100

    Update .travis.yml

commit ef3249f8224ff78df89a24e2113e6d03225cdc0f
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Mar 9 12:44:59 2016 +0100

    Add new ExonrankFilter object.

    + Add ExonrankFilter than enables filtering based on provided exon
      ranks/indexes.

commit 74a0281c6cf197a254fbb4e86de5b4a65904ffb9
Merge: 2037211 d162cb9
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Mar 9 11:23:44 2016 +0100

    Merge branch 'devel'

commit 20372113ee65fb6cc4c72ee042d831eb97a45c5c
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Feb 8 14:14:41 2016 +0100

    Next fix.

commit 430211e18f185b31b3589bb703c514cdca83669d
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Feb 8 14:09:38 2016 +0100

    Some more fixes: add install BioC deps.

commit a4746744d507c1abde84f3922f3eb53ada186f2a
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Feb 8 13:59:08 2016 +0100

    Update .travis.yml to metacran template.

commit ff0474bb46424d7b3b46a4fcfd2e15a12c181338
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Feb 8 12:22:38 2016 +0100

    Fix travis build error.

commit f01b65a842286be88c0f98c250b08216a7149b57
Merge: 5a7eef5 d19404e
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Feb 8 11:30:09 2016 +0100

    Merge branch 'devel'

commit 5a7eef55028a13a1ca281f34707d390edc1fc77a
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Feb 8 11:25:59 2016 +0100

    Fix failing RUnit test

commit 3d02ae2c946b92545232b8fc345a3aa0c6a91b10
Merge: 6ca7054 3365644
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Feb 4 08:34:33 2016 +0100

    Merge branch 'devel'

commit 6ca7054fff654af357fe790596358a8aa321e8a5
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Feb 4 08:29:13 2016 +0100

    Extend support to search by GRanges

    + exonsByOverlaps and transcriptByOverlaps methods.
    + Add support for GRanges of length > 1 in GRangesFilter.

commit 4b1bbda431ac1a2a040459f62e783413e6959f4e
Merge: 862fbce 6906b0f
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Feb 2 08:42:46 2016 +0100

    Merge branch 'devel'

commit 862fbce2e97a19f5ff3b6520ecb7279275aeef9c
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Feb 2 08:33:13 2016 +0100

    Add methodology to change seqlevel style

    + Implement methods seqlevelsStyle, seqlevelsStyls<-,
      supportedSeqlevelsStyles that enable to integrate EnsDb objects with
      annotation packages not using Ensembl chromosome names.
    + The seqinfo for results returned by methods such as genes, transcripts
      etc contain now only those seqnames that are present in the returned
      GRanges object.
    + Add more examples to the vignette and help pages.
    + Add more test cases.

commit cd1143a2c34739fead516f30c41a00171122b43c
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Jan 21 09:29:01 2016 +0100

    Crucial bug fix and new features

    + Fix a bug in fiveUTRsByTranscript and threeUTRsByTranscript that
      returned wrong UTRs for some cases in which the CDS was located within
      a single exon.
    + New method transcriptLengths to calculate length of transcript, UTR
      etc for transcripts.

commit 0cc2b55d86860b9504e99d59be208aa392836234
Merge: 1e4dfca 39a3366
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Jan 19 09:51:41 2016 +0100

    Merge branch 'devel'

commit 1e4dfca348024277a876a7c39906e5f1b8aa3b2f
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Tue Jan 19 09:42:54 2016 +0100

    Add ensDbFromGff and ensDbFromAH

    + Add methods ensDbFromGff and ensDbFromAH to build EnsDb objects from
      AnnotationHub or Ensembl provided files.
    + Fixed a bug resulting in wrong CDS for EnsDbs imported from GTF files.
    + getGenomeFaFile retrieves best matching FaFile if none for the
      specific Ensembl version is available.
    + Removed extractTranscriptSeqs method due to compatibility issues with
      GenomicFeatures package.

commit 1f7aa35c52cc4dd21abcc3756aa3e4be45a062e9
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Jan 7 14:36:49 2016 +0100

    Fix bug in select method.

    + select method now returns also the keytype column.

commit f6f51c3e0409a843900e6a7162a4c9f3a72b0594
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Jan 7 08:09:45 2016 +0100

    Implement methods from AnnotationDbi.

    + Implement methods columns, keys, keytypes and select.
    + Implement methods condition<- and value<- for BasicFilter.

commit 54db7a03bbec27719278271d124591212a7a89ca
Merge: 32b86af e5109e4
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Dec 21 15:10:38 2015 +0100

    Merge branch 'devel'

commit 32b86afe29f6289a3fa55345ce996bc533c19f02
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Mon Dec 21 15:02:36 2015 +0100

    Return search results from the EnsDb shiny app.

commit d1a97f8a492489544951e786a0009f978e8093bc
Merge: f2ec49a 55ecc17
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Dec 4 08:28:33 2015 +0100

    Merge branch 'devel'

commit f2ec49a2fef250994fb3442a3db4879de80d32da
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Fri Dec 4 08:22:42 2015 +0100

    Import seqlengths from GenomeInfoDb.

    + Fix that missing import based on a comment from Martin.

commit 640146b8322446ab6a3492187ce1dff87fdb6aac
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Dec 3 10:57:05 2015 +0100

    Badge fix.

commit b6024293212fcf32fce2d644bdd87282b5b72447
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Dec 3 10:40:59 2015 +0100

    Change to .travis.yml

commit 9318a012a04d497c521f4e244cf233c3d0669982
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Dec 3 10:06:50 2015 +0100

    Add codecov.io badge.

commit bb43c8ca5f4c0230cc14b9dfa7331e77950b51a6
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Dec 3 09:16:49 2015 +0100

    Trigger Travis CI test.

commit ea4c77aa5fec5ce96eb1723225c737da5a530494
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Dec 3 09:12:39 2015 +0100

    Add Travis CI check

commit 76a24ed93d9bcd6c20ab1bbb8cc3a10ba966ca21
Merge: 0b4d940 508fba0
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Dec 3 09:03:57 2015 +0100

    Merge branch 'devel'

commit 0b4d9400b3ad86f6a8ffbdd6bc3d12cee8c54b3a
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Thu Dec 3 08:55:38 2015 +0100

    Update vignette and fix unit test bug

    + Update the vignette.
    + Fix bug in an unit test.

commit 5de2001e2cb28faa3e241bfeb961ee963acfde92
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Dec 2 15:56:55 2015 +0100

    Another change to readme.

commit b1dd18ef830ec92f6a16a61ddd1ba00ecc8bab27
Author: jotsetung <johannes.rainer@gmail.com>
Date:   Wed Dec 2 15:54:59 2015 +0100

    Small change to readme.

commit 9521b7f19e17db5e1bb1e323171e56186c609363
Merge: 8630233 c5d11d3
Author: Johannes Rainer <jo@macbookjo.eurac.edu>
Date:   Tue Dec 1 14:17:58 2015 +0100

    Merge branch 'devel'

commit 8630233d6f907bf03ed7a8e4d6d75cb45aef833f
Merge: d743e96 46e90fc
Author: Johannes Rainer <jo@macbookjo.eurac.edu>
Date:   Tue Dec 1 13:23:16 2015 +0100

    Merge branch 'devel'

commit d743e968225d99ea6aecffba47c5609c8882f646
Author: Johannes Rainer <jo@macbookjo.eurac.edu>
Date:   Tue Dec 1 13:17:45 2015 +0100

    Fix a bug in ensDbFromGRanges

commit cf2f071317031d097be08ae6d58679ba4a294dae
Merge: 924e953 507ba0e
Author: Johannes Rainer <jo@macbookjo.eurac.edu>
Date:   Mon Nov 30 10:02:08 2015 +0100

    Merge branch 'devel'

commit 924e9530a6719cee4a43cddc9b4dd822c0233aa8
Author: Johannes Rainer <jo@macbookjo.eurac.edu>
Date:   Mon Nov 30 09:55:26 2015 +0100

    Add GRangesFilter and UCSC chromosome name support

    + Add new GRangesFilter allowing to filter using a GRanges object.
    + Add method "value" for BasicFilter object.
    + Move all generic methods to file "Generics.R".
    + Add support for UCSC chromosome names in filters and return UCSC
    chromosome names if option ucscChromosomeNames is TRUE.

From: jotsetung <johannes.rainer@gmail.com>
Revision: 129756
Author: a.gutierrez-sacristan
Date: 2017-05-19T15:47:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/psygenet2r/DESCRIPTION
Modified  /trunk/madman/Rpacks/psygenet2r/NAMESPACE
Modified  /trunk/madman/Rpacks/psygenet2r/NEWS
Modified  /trunk/madman/Rpacks/psygenet2r/R/psygenet2r.R
Modified  /trunk/madman/Rpacks/psygenet2r/man/DataGeNET.Psy-class.Rd
Modified  /trunk/madman/Rpacks/psygenet2r/man/JaccardIndexPsy-class.Rd
Modified  /trunk/madman/Rpacks/psygenet2r/man/enrichedPD-methods.Rd
Modified  /trunk/madman/Rpacks/psygenet2r/man/extract.Rd
Modified  /trunk/madman/Rpacks/psygenet2r/man/extractSentences.Rd
Modified  /trunk/madman/Rpacks/psygenet2r/man/geneAttrPlot-methods.Rd
Modified  /trunk/madman/Rpacks/psygenet2r/man/getUMLs-methods.Rd
Modified  /trunk/madman/Rpacks/psygenet2r/man/jaccardEstimation-methods.Rd
Modified  /trunk/madman/Rpacks/psygenet2r/man/ndisease.Rd
Modified  /trunk/madman/Rpacks/psygenet2r/man/ngene.Rd
Modified  /trunk/madman/Rpacks/psygenet2r/man/pantherGraphic-methods.Rd
Modified  /trunk/madman/Rpacks/psygenet2r/man/plot-DataGeNET.Psy-ANY-method.Rd
Modified  /trunk/madman/Rpacks/psygenet2r/man/plot-JaccardIndexPsy-ANY-method.Rd
Modified  /trunk/madman/Rpacks/psygenet2r/man/psygenetDisease-methods.Rd
Modified  /trunk/madman/Rpacks/psygenet2r/man/psygenetDiseaseSentences.Rd
Modified  /trunk/madman/Rpacks/psygenet2r/man/psygenetGene-methods.Rd
Modified  /trunk/madman/Rpacks/psygenet2r/man/psygenetGeneSentences.Rd
Modified  /trunk/madman/Rpacks/psygenet2r/man/qr.Rd
Modified  /trunk/madman/Rpacks/psygenet2r/man/topAnatEnrichment-methods.Rd
Update DECRIPTION.

Revision: 129755
Author: l.shepherd
Date: 2017-05-19T15:43:54+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationForge/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationForge/R/makeOrgPackageFromNCBI.R
Speed up makeOrgPackageFromNCBI recipe

  - avoid writing table on each iteration
Revision: 129753
Author: a.oles
Date: 2017-05-19T14:41:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/BiocWorkflowTools/DESCRIPTION
Modified  /trunk/madman/Rpacks/BiocWorkflowTools/NAMESPACE
Modified  /trunk/madman/Rpacks/BiocWorkflowTools/R/uploadToOverleaf.R
Modified  /trunk/madman/Rpacks/BiocWorkflowTools/man/uploadToOverleaf.Rd
Use alternative approach to initialize Overleaf project's git repo
Revision: 129749
Author: s.pollack
Date: 2017-05-19T13:43:40+00:00
Paths:
Modified  /trunk/madman/Rpacks/bumphunter/DESCRIPTION
increment version number for bugfix

From: sampoll <sampoll@users.noreply.github.com>
Revision: 129748
Author: s.pollack
Date: 2017-05-19T13:43:34+00:00
Paths:
Modified  /trunk/madman/Rpacks/bumphunter/DESCRIPTION
Modified  /trunk/madman/Rpacks/bumphunter/NAMESPACE
Modified  /trunk/madman/Rpacks/bumphunter/R/matchGenes.R
Modified  /trunk/madman/Rpacks/bumphunter/man/annotateTranscripts.Rd
Modified  /trunk/madman/Rpacks/bumphunter/tests/testthat/test_annotation.R
v1.17.2 -- Adds supported for TxDb objects with gene ids from ENSEMBL/GENCODE

This commit resolves https://github.com/rafalab/bumphunter/issues/15 by
adding the arguments `mappingInfo` and `simplifyGeneID` to
`annotateTranscripts()`. `mappingInfo` is a named list whose elements are passed
to `AnnotateDbi::mapIds()` for more flexible gene id matching between a given
TxDb object and the organism package (like org.Hs.eg.db). `simplifyGeneId` is
a logical and if TRUE gene ids like `ENSTsomething.8_etc` get simplified to
`ENSTsomething`. This allows working with TxDb objects created from
GENCODE GTF files and matching then to org.Hs.eg.db as if the ids were
ENSEMBL gene ids.

A unit test checking the new changes has been added as well.

A check and build reveals no new notes/warnings/errors.

```
$ R CMD build --keep-empty-dirs --no-resave-data bumphunter
Loading required package: colorout
* checking for file ‘bumphunter/DESCRIPTION’ ... OK
* preparing ‘bumphunter’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘bumphunter_1.17.2.tar.gz’

$ R CMD check --no-vignettes --timings bumphunter_1.17.2.tar.gz
Loading required package: colorout
* using log directory ‘/Users/lcollado/Dropbox/Code/bumphunter.Rcheck’
* using R version 3.4.0 (2017-04-21)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bumphunter/DESCRIPTION’ ... OK
* this is package ‘bumphunter’ version ‘1.17.2’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘S4Vectors’ ‘IRanges’ ‘GenomeInfoDb’ ‘GenomicRanges’ ‘foreach’
  ‘iterators’ ‘parallel’ ‘locfit’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘bumphunter’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘doParallel:::.options’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bumphunterEngine: no visible binding for global variable ‘bootstraps’
Undefined global functions or variables:
  bootstraps
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
  Running ‘test-all.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/lcollado/Dropbox/Code/bumphunter.Rcheck/00check.log’
for details.

```

From: Leonardo Collado Torres <lcollado@jhsph.edu>
Revision: 129747
Author: s.pollack
Date: 2017-05-19T13:43:25+00:00
Paths:
Modified  /trunk/madman/Rpacks/bumphunter/DESCRIPTION
Modified  /trunk/madman/Rpacks/bumphunter/R/bumphunter.R
Merge with Bioconductor devel brach

From: Samuela Pollack <sampoll@users.noreply.github.com>
Revision: 129746
Author: s.pollack
Date: 2017-05-19T13:19:08+00:00
Paths:
Modified  /trunk/madman/Rpacks/bumphunter/README.md
whitespace change; checking permissions
Revision: 129745
Author: m.lawrence
Date: 2017-05-19T13:02:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/DESCRIPTION
version bump
Revision: 129744
Author: m.lawrence
Date: 2017-05-19T13:02:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/R/List-class-leftovers.R
stack() always puts the grouping variable first
Revision: 129743
Author: m.lawrence
Date: 2017-05-19T13:01:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/man/AtomicList-utils.Rd
diff S3 method man page fixes
Revision: 129742
Author: m.lawrence
Date: 2017-05-19T12:55:15+00:00
Paths:
Modified  /trunk/madman/Rpacks/IRanges/NAMESPACE
Modified  /trunk/madman/Rpacks/IRanges/R/AtomicList-utils.R
simplify diff S3 methods on AtomicLists
Revision: 129741
Author: l.gatto
Date: 2017-05-19T09:26:30+00:00
Paths:
Modified  /trunk/madman/Rpacks/pRoloc/DESCRIPTION
Modified  /trunk/madman/Rpacks/pRoloc/NEWS
Modified  /trunk/madman/Rpacks/pRoloc/NEWS.md
Modified  /trunk/madman/Rpacks/pRoloc/R/phenodisco.R
Modified  /trunk/madman/Rpacks/pRoloc/man/phenoDisco.Rd
fix conflicts

From: Laurent <lg390@cam.ac.uk>
Revision: 129740
Author: l.revilla
Date: 2017-05-19T08:36:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/BioCor/.Rbuildignore
Added  /trunk/madman/Rpacks/BioCor/.github
Added  /trunk/madman/Rpacks/BioCor/.github/CONTRIBUTING.md
Added  /trunk/madman/Rpacks/BioCor/.github/ISSUE_TEMPLATE.md
Modified  /trunk/madman/Rpacks/BioCor/.gitignore
Modified  /trunk/madman/Rpacks/BioCor/DESCRIPTION
Modified  /trunk/madman/Rpacks/BioCor/NAMESPACE
Modified  /trunk/madman/Rpacks/BioCor/NEWS
Modified  /trunk/madman/Rpacks/BioCor/R/AintoB.R
Modified  /trunk/madman/Rpacks/BioCor/R/clusterGeneSim.R
Modified  /trunk/madman/Rpacks/BioCor/R/clusterSim.R
Modified  /trunk/madman/Rpacks/BioCor/R/combineScores.R
Added  /trunk/madman/Rpacks/BioCor/R/combineSources.R
Modified  /trunk/madman/Rpacks/BioCor/R/diceSim.R
Modified  /trunk/madman/Rpacks/BioCor/R/geneSim.R
Modified  /trunk/madman/Rpacks/BioCor/R/pathSim.R
Modified  /trunk/madman/Rpacks/BioCor/R/zzz.R
Modified  /trunk/madman/Rpacks/BioCor/README.md
Modified  /trunk/madman/Rpacks/BioCor/man/clusterGeneSim.Rd
Modified  /trunk/madman/Rpacks/BioCor/man/clusterSim.Rd
Modified  /trunk/madman/Rpacks/BioCor/man/combineScores.Rd
Added  /trunk/madman/Rpacks/BioCor/man/combineSources.Rd
Modified  /trunk/madman/Rpacks/BioCor/man/diceSim.Rd
Modified  /trunk/madman/Rpacks/BioCor/man/geneSim.Rd
Modified  /trunk/madman/Rpacks/BioCor/man/pathSim.Rd
Modified  /trunk/madman/Rpacks/BioCor/tests/testthat/test_clusterGeneSim.R
Modified  /trunk/madman/Rpacks/BioCor/tests/testthat/test_clusterSim.R
Modified  /trunk/madman/Rpacks/BioCor/tests/testthat/test_combineScores.R
Added  /trunk/madman/Rpacks/BioCor/tests/testthat/test_combineSources.R
Modified  /trunk/madman/Rpacks/BioCor/tests/testthat/test_diceSim.R
Modified  /trunk/madman/Rpacks/BioCor/tests/testthat/test_geneSim.R
Modified  /trunk/madman/Rpacks/BioCor/tests/testthat/test_pathSim.R
Modified  /trunk/madman/Rpacks/BioCor/tests/testthat/test_similarities.R
Modified  /trunk/madman/Rpacks/BioCor/tests/testthat/test_weighted.R
Modified  /trunk/madman/Rpacks/BioCor/vignettes/BioCor.Rmd
Bump new version with changes from master
Revision: 129739
Author: l.revilla
Date: 2017-05-19T08:36:31+00:00
Paths:
Modified  /trunk/madman/Rpacks/BioCor/DESCRIPTION
Modified  /trunk/madman/Rpacks/BioCor/vignettes/BioCor.Rmd
Correct version numbering and correct typo in vignette
Revision: 129738
Author: hpages
Date: 2017-05-19T06:39:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/HDF5Array/R/dump-management.R
cleaner code
Revision: 129737
Author: hpages
Date: 2017-05-19T06:15:14+00:00
Paths:
Modified  /trunk/madman/Rpacks/HDF5Array/R/dump-management.R
Modified  /trunk/madman/Rpacks/HDF5Array/R/utils.R
Modified  /trunk/madman/Rpacks/HDF5Array/R/writeHDF5Array.R
a couple of minor tweaks
Revision: 129736
Author: t.silva
Date: 2017-05-19T04:17:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinks/vignettes/download_prepare.Rmd
Modified  /trunk/madman/Rpacks/TCGAbiolinks/vignettes/mutation.Rmd
updat
Revision: 129735
Author: t.silva
Date: 2017-05-19T04:12:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/TCGAbiolinks/vignettes/download_prepare.Rmd
updates
Revision: 129734
Author: hpages
Date: 2017-05-19T03:35:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/HDF5Array/R/dump-management.R
Modified  /trunk/madman/Rpacks/HDF5Array/R/utils.R
Modified  /trunk/madman/Rpacks/HDF5Array/R/zzz.R
Add set/getHDF5DumpFile(). Not exported/documented yet.
Revision: 129733
Author: stvjc
Date: 2017-05-19T01:53:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/ldblock/DESCRIPTION
Modified  /trunk/madman/Rpacks/ldblock/R/s3_1kg.R
some changes to stack1kg to reflect new work on VcfStack in GenomicFiles
Revision: 129725
Author: h.corradabravo
Date: 2017-05-18T23:53:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/metavizr/DESCRIPTION
version bump

From: hcorrada <hcorrada@gmail.com>
Revision: 129724
Author: h.corradabravo
Date: 2017-05-18T23:51:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/metavizr/R/EpivizMetagenomicsData-class.R
fix response format for PCA

From: Jayaram Kancherla <jayaram.kancherla@gmail.com>
Revision: 129723
Author: h.corradabravo
Date: 2017-05-18T23:50:57+00:00
Paths:
Modified  /trunk/madman/Rpacks/metavizr/R/EpivizMetagenomicsData-class.R
Modified  /trunk/madman/Rpacks/metavizr/tests/testthat/test-EpivizMetagenomicsData_class.R
Fixing PCA and add tests

From: Justin Wagner <jmwagner@umd.edu>
Revision: 129722
Author: h.corradabravo
Date: 2017-05-18T23:50:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/metavizr/R/EpivizMetagenomicsData-class.R
Updating leaf_sample_count table creation to take all spline values

From: Justin Wagner <jmwagner@umd.edu>
Revision: 129721
Author: h.corradabravo
Date: 2017-05-18T23:50:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/metavizr/R/EpivizMetagenomicsData-class.R
support the lineage bar on icicle - add levels, root lineage label on getHierarchy calls

From: Jayaram Kancherla <jayaram.kancherla@gmail.com>
Revision: 129720
Author: h.corradabravo
Date: 2017-05-18T23:50:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/metavizr/R/EpivizMetagenomicsData-class.R
send annotationson get_measurements

From: Jayaram Kancherla <jayaram.kancherla@gmail.com>
Revision: 129719
Author: h.corradabravo
Date: 2017-05-18T23:50:32+00:00
Paths:
Modified  /trunk/madman/Rpacks/metavizr/R/EpivizMetagenomicsData-class.R
Modified  /trunk/madman/Rpacks/metavizr/R/startMetaviz.R
Removing start and end arguments for getPCA call from app

From: Justin Wagner <jmwagner@umd.edu>
Revision: 129718
Author: m.lawrence
Date: 2017-05-18T22:47:56+00:00
Paths:
Modified  /trunk/madman/Rpacks/gmapR/DESCRIPTION
version bump
Revision: 129717
Author: m.lawrence
Date: 2017-05-18T22:47:22+00:00
Paths:
Modified  /trunk/madman/Rpacks/gmapR/R/GmapGenome-class.R
Modified  /trunk/madman/Rpacks/gmapR/R/gmap_build-command.R
normalize path to fasta file for gmap_build

Needed because we are running it inside a temporary directory. That
logic is now passed down to gmap_build() from referenceSequence<-().
Revision: 129714
Author: hpages
Date: 2017-05-18T21:52:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/HDF5Array/R/dump-management.R
Modified  /trunk/madman/Rpacks/HDF5Array/R/writeHDF5Array.R
rename internal utility append_dataset_creation_to_dump_logfile -> append_dataset_creation_to_dump_log
Revision: 129712
Author: hpages
Date: 2017-05-18T21:27:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/HDF5Array/DESCRIPTION
Modified  /trunk/madman/Rpacks/HDF5Array/NAMESPACE
add missing import
Revision: 129710
Author: hpages
Date: 2017-05-18T21:23:03+00:00
Paths:
Modified  /trunk/madman/Rpacks/HDF5Array/DESCRIPTION
Modified  /trunk/madman/Rpacks/HDF5Array/R/dump-management.R
Modified  /trunk/madman/Rpacks/HDF5Array/man/dump-management.Rd
showHDF5DumpLog() now returns the dump log in an invisible data frame

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