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
Maintainer
LicenseArtistic-2.0
Version1.1.3
URL https://mdeber.github.io
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
install.packages("remotes")
remotes::install_github("mdeber/BRGenomics")
mdeber/BRGenomics documentation built on Sept. 2, 2020, 1:14 a.m.