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.
|Author||Mike DeBerardine [aut, cre]|
|Bioconductor views||ATACSeq ChIPSeq Coverage DataImport GeneExpression GeneRegulation Normalization RNASeq Sequencing Software Transcription|
|Maintainer||Mike DeBerardine <firstname.lastname@example.org>|
|Package repository||View on Bioconductor|
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