recipe bioconductor-exomepeak2

Bias Awared Peak Calling and Quantification for MeRIP-Seq

Homepage

https://bioconductor.org/packages/3.11/bioc/html/exomePeak2.html

License

GPL (>= 2)

Recipe

/bioconductor-exomepeak2/meta.yaml

exomePeak2 provides bias awared quantification and peak detection on Methylated RNA immunoprecipitation sequencing data (MeRIP-Seq). MeRIP-Seq is a commonly applied sequencing technology to measure the transcriptome-wide location and abundance of RNA modification sites under a given cellular condition. However, the quantification and peak calling in MeRIP-Seq are sensitive to PCR amplification bias which is prevalent in next generation sequencing (NGS) techniques. In addition, the RNA-Seq based count data exhibits biological variation in small reads count. exomePeak2 collectively address these challanges by introducing a rich set of robust data science models tailored for MeRIP-Seq. With exomePeak2, users can perform peak calling, modification site quantification, and differential analysis with a straightforward one-step function. Alternatively, users could define personalized methods for their own analysis through multi-step functions and diagnostic plots.

package bioconductor-exomepeak2

(downloads) docker_bioconductor-exomepeak2

Versions

1.0.0-0

Depends
Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-exomepeak2

and update with:

conda update bioconductor-exomepeak2

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-exomepeak2:<tag>

(see bioconductor-exomepeak2/tags for valid values for <tag>)