Package Recipe 'bioconductor-brgenomics'

recipe bioconductor-brgenomics

Tools for the Efficient Analysis of High-Resolution Genomics Data

Homepage:: https://bioconductor.org/packages/3.18/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:

1.13.0-0, 1.12.0-0, 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:

on bioconductor-deseq2 >=1.42.0,<1.43.0
on bioconductor-genomeinfodb >=1.38.0,<1.39.0
on bioconductor-genomicalignments >=1.38.0,<1.39.0
on bioconductor-genomicranges >=1.54.0,<1.55.0
on bioconductor-iranges >=2.36.0,<2.37.0
on bioconductor-rsamtools >=2.18.0,<2.19.0
on bioconductor-rtracklayer >=1.62.0,<1.63.0
on bioconductor-s4vectors >=0.40.0,<0.41.0
on bioconductor-summarizedexperiment >=1.32.0,<1.33.0
on r-base >=4.3,<4.4.0a0

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-brgenomics

to add into an existing workspace instead, run:

pixi add bioconductor-brgenomics

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-brgenomics

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-brgenomics

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-brgenomics/README.html)