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. |