mdeber/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.

Getting started

Package details

Bioconductor views ATACSeq ChIPSeq Coverage DataImport GeneExpression GeneRegulation Normalization RNASeq Sequencing Software Transcription
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
mdeber/BRGenomics documentation built on Sept. 2, 2020, 1:14 a.m.