Man pages for BRGenomics
Tools for the Efficient Analysis of High-Resolution Genomics Data

applyNFsGRangesApply normalization factors to GRanges object
binNDimensionsGenerating and Aggregating Data Within N-dimensional Bins
bootstrap-signal-by-positionBootstrapping Mean Signal by Position for Metaplotting
BRGenomics-packageBRGenomics: Tools for the Efficient Analysis of...
genebodiesExtract Genebodies
getCountsByPositionsGet signal counts at each position within regions of interest
getCountsByRegionsGet signal counts in regions of interest
getDESeqDataSetGet DESeqDataSet objects for downstream analysis
getDESeqResultsGet DESeq2 results using reduced dispersion matrices
getMaxPositionsBySignalFind sites with max signal in regions of interest
getPausingIndicesCalculate pausing indices from user-supplied promoters &...
getSpikeInCountsFiltering and counting spike-in reads
getSpikeInNFsCalculating spike-in normalization factors
getStrandedCoverageGet strand-specific coverage
import_bamImport bam files
import-functionsImport basepair-resolution files
intersectByGeneIntersect or reduce ranges according to gene names
makeGRangesBRGConstructing and checking for base-pair resolution GRanges...
mergeGRangesDataMerge GRanges objects
mergeReplicatesMerge replicates of basepair-resolution GRanges objects
PROseq-dataPRO-seq data from Drosophila S2 cells
subsampleBySpikeInRandomly subsample reads according to spike-in normalization
subsampleGRangesRandomly subsample reads from GRanges dataset
subsetRegionsBySignalSubset regions of interest by quantiles of overlapping signal
tidyChromosomesRemove odd chromosomes from GRanges objects
txs_dm6_chr4Ensembl transcripts for Drosophila melanogaster, dm6,...
BRGenomics documentation built on Nov. 8, 2020, 8:03 p.m.