Package Recipe 'bioconductor-baalchip'

recipe bioconductor-baalchip

BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/BaalChIP.html
License:: Artistic-2.0
Recipe:: /bioconductor-baalchip/meta.yaml
Links:: biotools: baalchip, doi: 10.1186/s13059-017-1165-7

The package offers functions to process multiple ChIP-seq BAM files and detect allele-specific events. Computes allele counts at individual variants (SNPs/SNVs), implements extensive QC steps to remove problematic variants, and utilizes a bayesian framework to identify statistically significant allele- specific events. BaalChIP is able to account for copy number differences between the two alleles, a known phenotypical feature of cancer samples.

package bioconductor-baalchip¶

Versions:

1.36.0-0, 1.32.0-0, 1.28.0-0, 1.26.0-0, 1.24.0-0, 1.20.0-0, 1.18.0-0, 1.16.0-1, 1.16.0-0,

1.36.0-0, 1.32.0-0, 1.28.0-0, 1.26.0-0, 1.24.0-0, 1.20.0-0, 1.18.0-0, 1.16.0-1, 1.16.0-0, 1.14.0-0, 1.12.0-0, 1.10.0-1, 1.8.0-0, 1.6.0-0, 1.4.0-0

Depends:

on bioconductor-genomeinfodb >=1.46.0,<1.47.0
on bioconductor-genomicalignments >=1.46.0,<1.47.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-rsamtools >=2.26.0,<2.27.0
on r-base >=4.5,<4.6.0a0
on r-coda
on r-doby
on r-doparallel
on r-foreach
on r-ggplot2
on r-reshape2
on r-scales

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-baalchip

to add into an existing workspace instead, run:

pixi add bioconductor-baalchip

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-baalchip

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-baalchip

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-baalchip:<tag>

(see bioconductor-baalchip/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-baalchip/README.html)