recipe bioconductor-brgenomics

Tools for the Efficient Analysis of High-Resolution Genomics Data

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/BRGenomics.html

License:

Artistic-2.0

Recipe:

/bioconductor-brgenomics/meta.yaml

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.

package bioconductor-brgenomics

Versions:

1.10.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1,  1.2.0-0,  1.0.0-0

Depends:

• bioconductor-deseq2 >=1.38.0,<1.39.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicalignments >=1.34.0,<1.35.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-rsamtools >=2.14.0,<2.15.0

• bioconductor-rtracklayer >=1.58.0,<1.59.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-base >=4.2,<4.3.0a0

Required By:

• bioconductor-epicompare

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-brgenomics

and update with:

conda update bioconductor-brgenomics

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-brgenomics:<tag>

(see bioconductor-brgenomics/tags for valid values for <tag>)

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