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 |
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 |