Changes in version 1.36.99 o IMPROVED Version number changed to reflect Bioconductor repository Changes in version 1.5.11 o IMPROVED ANNMAP-121 The data is now cached in a dedicated directory instead of in the home directory o IMPROVED ANNMAP-121 URLs for the project and the download location for the database was updated Changes in version 1.5.10 o IMPROVED ANNMAP-121 Allow setting of WS base url for local testing Changes in version 1.5.8 o IMPROVED ANNMAP-119 as.vector=TRUE results are now named o IMPROVED ANNMAP-120 genomeToTranscriptCoords could handle coding regions Changes in version 1.5.7 o BUG Check for uniqueness in transcriptToCodingExon, transcriptToCodingRange, transcriptToUtrExon and transcriptToUtrRange Changes in version 1.5.6 o NEW Added transcriptToUtrExon o IMPROVED Sequence removed from transcriptToCodingExon Changes in version 1.5.5 o IMPROVED ANNMAP-115 Added method geneToGeneRegionTrack to generate a list of Gviz GeneRegionTrack elements that can be passed to plotTracks Changes in version 1.5.4 o BUG ANNMAP-118 transcriptToCodingRange( ..., end='3' ) returns whole transcript for untranslated transcripts. o IMPROVED ANNMAP-114 Added additional logging when using webservice o IMPROVED ANNMAP-116 Introduce function(s) to calculate the coding length of a gene(s) - See: ?nonIntronicGeneLength and ?nonIntronicTranscriptLength. Changes in version 1.5.3 o IMPROVED ANNMAP-114 Added additional logging when using webservice o IMPROVED ANNMAP-113 Added documentation to cookbook for webservice o IMPROVED webservice json to data.frame speed improvements Changes in version 1.2.1 o BUG ANNMAP-112 transcriptCoordsToGenome and proteinCoordsToGenome both failed when returning a GRanges object as I had strand as a numeric, rather than an integer. Changes in version 1.1.1 o IMPROVED genomicPlot when passed a .genes data.frame used to call geneDetails on it to ensure the data was in the correct format. This has been removed, so that you can pass custom regions in and have them plotted on the graph. Changes in version 0.99.3 o BUG ANNMAP-110 XXXInRange( NULL ) used to throw an error. It now returns NULL. o BUG ANNMAP-111 Fix crash when translation data is incorrect and causes us to fall off the translation exon when finding the UTR/Coding range. Changes in version 0.99.2 o BUG ANNMAP-109 geneToSymbol when passed a vector of gene IDs, returned the symbols in the order of the genes start location rather than the order the function was called with. Changes in version 0.99.1 o BUG ANNMAP-101 ngsBridgePlot called with no genes in range had a huge border. o BUG ANNMAP-106 Empty ngsBridgePlot trace should draw line at 0. o BUG ANNMAP-107 transcriptToCodingRange was very slow. Changes in version 0.99.0 o NEW Initial Release to Bioconductor o BUG ANNMAP-98 A call to transcriptToTranslatedprobes for transcripts in HPRT1 caused a crash Changes in version 0.9.16 o BUG ANNMAP-97 geneToExonProbeset threw an error when as.vector=TRUE Changes in version 0.9.15 o NEW ANNMAP-94 Added annmapAddConnection method for setting up databases. Changes in version 0.9.14 o NEW ANNMAP-90 Added generateBridgeData method for helping with BAM file imports. o IMPROVED ANNMAP-93 Refactored out some NCBI->Ensembl seqname mapping functions. o IMPROVED ANNMAP-84 Added ngsBridgePlot examples to the cookbook. Changes in version 0.9.13 o IMPROVED ANNMAP-78 Cookbook now appears when vignette( package='annmap' ) is called. Changes in version 0.9.12 o IMPROVED ANNMAP-74, ANNMAP-75, ANNMAP-76; Fixed warnings and notes when using R-2.15 Changes in version 0.9.11 o IMPROVED ANNMAP-73 Methods generalisedNameToNCBI, generalisedNameToEnsembl, seqnameMapping, seqnamesToNCBI and seqnamesToEnsembl added to allow easy renaming of the seqnames column of GRanges data. Changes in version 0.9.10 o IMPROVED ANNMAP-71 Bug in geneToSymbol fixed Changes in version 0.9.9 o IMPROVED ANNMAP-63 We now use GenomicRanges instead of IRanges Changes in version 0.9.8 o IMPROVED ANNMAP-58 Added 4 pos translation documentation to cookbook o BUG ANNMAP-60 Webservice tests were failing o BUG ANNMAP-54 geneToExonProbeset didn't support as.vector Changes in version 0.9.7 o BUG ANNMAP-48 Error in proteinCoordsToGenome in annmap o BUG ANNMAP-47 annmapGenePlot fails to show individual transcripts o IMPROVED ANNMAP-45 Added a NEWS.Rd file to inst Changes in version 0.9.6 o BUG Fixed ANNMAP-44; genomicPlot crashes when called with very small overlapped areas Changes in version 0.9.5 o IMPROVED ANNMAP-41; All InRange methods are now S3 methods which work with character, data.frame or RangedData (see ?annmap.range). o IMPROVED ANNMAP-42; genomicPlot highlights 'colour' column is now 'col' as with all other methods. o BUG ANNMAP-40; genomicPlot crashes if highlights data.frame has unexpected columns.