# Visualization and annotation of read signal over genomic ranges with profileplyr

## Documentation for package ‘profileplyr’ version 1.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## 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