Visualization and annotation of read signal over genomic ranges
with profileplyr
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Documentation for package ‘profileplyr’ version 1.24.1
Help Pages
| annotateRanges | Annotate profileplyr ranges to genes using ChIPseeker |
| annotateRanges-method | Annotate profileplyr ranges to genes using ChIPseeker |
| annotateRanges_great | Annotate profileplyr ranges to genes using rGREAT |
| annotateRanges_great-method | Annotate profileplyr ranges to genes using rGREAT |
| as_profileplyr | Import ChIPprofile object to profileplyr |
| BamBigwig_to_chipProfile | BamBigwig_to_chipProfile |
| c-method | Join, subset and manipulate ChIPprofile objects |
| clusterRanges | Cluster Ranges |
| clusterRanges-method | Cluster Ranges |
| convertToEnrichedHeatmapMat | export a profileplyr object to a list of matrices that can be used as an input for EnrichedHeatmap |
| convertToEnrichedHeatmapMat-method | export a profileplyr object to a list of matrices that can be used as an input for EnrichedHeatmap |
| export_deepToolsMat | Export and import profileplyr from/to deeptools |
| export_deepToolsMat-method | Export and import profileplyr from/to deeptools |
| generateEnrichedHeatmap | generateEnrichedHeatmap |
| generateProfilePlot | Import ChIPprofile object to profileplyr |
| gene_list_character | Character vector of the top differentially expressed genes from hindbrain versus liver as measured by RNA-seq |
| gene_list_dataframe | Dataframe of top differentially expressed genes from hindbrain versus liver as measured by RNA-seq |
| groupBy | group the rows and ranges of the profileplyr object |
| groupBy-method | group the rows and ranges of the profileplyr object |
| import_deepToolsMat | Export and import profileplyr from/to deeptools |
| inherit_group_function | Redundant code for inheriting grouping wrapped into subsetbyRangeOverlap() or subsetbyGeneListOverlap() functions |
| K27ac_GRlist_hind_liver_top5000 | GRangesList of the top 5000 H3K27ac peaks from hindbrain and liver downloaded from ENCODE |
| orderBy | choose the column by which to order the ranges by within each group |
| orderBy-method | choose the column by which to order the ranges by within each group |
| params | Retrieve and set parameters in profileplyr object |
| profileplyr-class | Join, subset and manipulate ChIPprofile objects |
| sampleData | Retrieve and set sample data in profileplyr object |
| sampleData-method | Retrieve and set sample data in profileplyr object |
| sampleData<- | Retrieve and set sample data in profileplyr object |
| sampleData<--method | Retrieve and set sample data in profileplyr object |
| subsetbyGeneListOverlap | Subset ranges based on overlap with lists of Gene sets |
| subsetbyRangeOverlap | Subset ranges based on overlap with a GRanges object |
| subset_GR_GL_common_top | Redundant code wrapped into subsetbyRangeOverlap() or subsetbyGeneListOverlap() functions |
| summarize | summarize the rows of a deepTools matrix |
| summarize-method | summarize the rows of a deepTools matrix |
| [-method | Join, subset and manipulate ChIPprofile objects |