Package: BRGenomics 1.17.0

Mike DeBerardine

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

This package provides useful and efficient utilites for the analysis of high-resolution genomic data using standard Bioconductor methods and classes. BRGenomics is feature-rich and simplifies a number of post-alignment processing steps and data handling. Emphasis is on efficient analysis of multiple datasets, with support for normalization and blacklisting. Included are functions for: spike-in normalizing data; generating basepair-resolution readcounts and coverage data (e.g. for heatmaps); importing and processing bam files (e.g. for conversion to bigWig files); generating metaplots/metaprofiles (bootstrapped mean profiles) with confidence intervals; conveniently calling DESeq2 without using sample-blind estimates of genewise dispersion; among other features.

Authors:Mike DeBerardine [aut, cre]

BRGenomics_1.17.0.tar.gz
BRGenomics_1.17.0.zip(r-4.3)
BRGenomics_1.17.0.tgz(r-4.3-any)
BRGenomics_1.17.0.tar.gz(r-4.5-noble)BRGenomics_1.17.0.tar.gz(r-4.4-noble)
BRGenomics_1.17.0.tgz(r-4.4-emscripten)BRGenomics_1.17.0.tgz(r-4.3-emscripten)
BRGenomics.pdf |BRGenomics.html✨
BRGenomics/json (API)
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Bug tracker:https://github.com/mdeber/brgenomics/issues

On BioConductor:BRGenomics-1.17.0(bioc 3.20)BRGenomics-1.16.0(bioc 3.19)

bioconductor-package

35 exports 0.82 score 78 dependencies 1 dependents

Last updated 2 months agofrom:34753d5034

Exports:aggregateByNdimBinsapplyNFsGRangesbinNdimensionsdensityInNdimBinsgenebodiesgetCountsByPositionsgetCountsByRegionsgetDESeqDataSetgetDESeqResultsgetMaxPositionsBySignalgetPausingIndicesgetSpikeInCountsgetSpikeInNFsgetSpikeInReadsgetStrandedCoverageimport_bamimport_bam_ATACseqimport_bam_PROcapimport_bam_PROseqimport_bedGraphimport_bigWigintersectByGeneisBRGmakeGRangesBRGmergeGRangesDatamergeReplicatesmetaSubsamplemetaSubsampleMatrixreduceByGeneremoveSpikeInReadsspikeInNormGRangessubsampleBySpikeInsubsampleGRangessubsetRegionsBySignaltidyChromosomes

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsclicodetoolscolorspacecpp11crayoncurlDelayedArrayDESeq2fansifarverformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigR6RColorBrewerRcppRcppArmadilloRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsscalessnowSparseArraySummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryamlzlibbioc