Package Recipe 'bioconductor-exomepeak2'

recipe bioconductor-exomepeak2

Peak Calling and differential analysis for MeRIP-Seq

Homepage:: https://bioconductor.org/packages/3.18/bioc/html/exomePeak2.html
License:: Artistic-2.0
Recipe:: /bioconductor-exomepeak2/meta.yaml

exomePeak2 provides peak detection and differential methylation for Methylated RNA Immunoprecipitation Sequencing (MeRIP-Seq) data. MeRIP-Seq is a commonly applied sequencing assay that measures the location and abundance of RNA modification sites under specific cellular conditions. The technique is sensitive to PCR amplification biases commonly found in NGS data. In addition, the efficiency of immunoprecipitation often varies between different IP samples. exomePeak2 can perform peak calling and differential analysis independent of GC content bias and IP efficiency changes.

package bioconductor-exomepeak2¶

Versions:

1.14.3-0, 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-biocgenerics >=0.48.0,<0.49.0
on bioconductor-biocparallel >=1.36.0,<1.37.0
on bioconductor-biostrings >=2.70.0,<2.71.0
on bioconductor-bsgenome >=1.70.0,<1.71.0
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-genomicfeatures >=1.54.0,<1.55.0
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
on r-ggplot2
on r-magrittr
on r-mclust
on r-speedglm

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-exomepeak2

to add into an existing workspace instead, run:

pixi add bioconductor-exomepeak2

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-exomepeak2

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-exomepeak2

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-exomepeak2:<tag>

(see bioconductor-exomepeak2/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-exomepeak2/README.html)