Tools for the Efficient Analysis of High-Resolution Genomics Data

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Documentation for package ‘BRGenomics’ version 1.10.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

BRGenomics-package	BRGenomics: Tools for the Efficient Analysis of High-Resolution Genomics Data
aggregateByNdimBins	Generating and Aggregating Data Within N-dimensional Bins
applyNFsGRanges	Apply normalization factors to GRanges object
binNdimensions	Generating and Aggregating Data Within N-dimensional Bins
bootstrap-signal-by-position	Bootstrapping Mean Signal by Position for Metaplotting
BRGenomics	BRGenomics: Tools for the Efficient Analysis of High-Resolution Genomics Data
densityInNdimBins	Generating and Aggregating Data Within N-dimensional Bins
genebodies	Extract Genebodies
getCountsByPositions	Get signal counts at each position within regions of interest
getCountsByRegions	Get signal counts in regions of interest
getDESeqDataSet	Get DESeqDataSet objects for downstream analysis
getDESeqResults	Get DESeq2 results using reduced dispersion matrices
getMaxPositionsBySignal	Find sites with max signal in regions of interest
getPausingIndices	Calculate pausing indices from user-supplied promoters & genebodies
getSpikeInCounts	Filtering and counting spike-in reads
getSpikeInNFs	Calculating spike-in normalization factors
getSpikeInReads	Filtering and counting spike-in reads
getStrandedCoverage	Get strand-specific coverage
import-functions	Import basepair-resolution files
import_bam	Import bam files
import_bam_ATACseq	Import bam files
import_bam_PROcap	Import bam files
import_bam_PROseq	Import bam files
import_bedGraph	Import basepair-resolution files
import_bigWig	Import basepair-resolution files
intersectByGene	Intersect or reduce ranges according to gene names
isBRG	Constructing and checking for base-pair resolution GRanges objects
makeGRangesBRG	Constructing and checking for base-pair resolution GRanges objects
mergeGRangesData	Merge GRanges objects
mergeReplicates	Merge replicates of basepair-resolution GRanges objects
metaSubsample	Bootstrapping Mean Signal by Position for Metaplotting
metaSubsampleMatrix	Bootstrapping Mean Signal by Position for Metaplotting
PROseq	PRO-seq data from Drosophila S2 cells
PROseq-data	PRO-seq data from Drosophila S2 cells
PROseq_paired	PRO-seq data from Drosophila S2 cells
reduceByGene	Intersect or reduce ranges according to gene names
removeSpikeInReads	Filtering and counting spike-in reads
spikeInNormGRanges	Calculating spike-in normalization factors
subsampleBySpikeIn	Randomly subsample reads according to spike-in normalization
subsampleGRanges	Randomly subsample reads from GRanges dataset
subsetRegionsBySignal	Subset regions of interest by quantiles of overlapping signal
tidyChromosomes	Remove odd chromosomes from GRanges objects
txs_dm6_chr4	Ensembl transcripts for Drosophila melanogaster, dm6, chromosome 4.