recipe bioconductor-exomepeak2

Bias-aware Peak Calling and Quantification for MeRIP-Seq

Homepage

https://bioconductor.org/packages/3.14/bioc/html/exomePeak2.html

License

GPL (>= 2)

Recipe

/bioconductor-exomepeak2/meta.yaml

exomePeak2 provides bias-aware quantification and peak detection for Methylated RNA immunoprecipitation sequencing data (MeRIP-Seq). MeRIP-Seq is a commonly applied sequencing technology that can measure the location and abundance of RNA modification sites under given cell line conditions. However, quantification and peak calling in MeRIP-Seq are sensitive to PCR amplification biases, which generally present in next-generation sequencing (NGS) technologies. In addition, the count data generated by RNA-Seq exhibits significant biological variations between biological replicates. exomePeak2 collectively address the challenges by introducing a series of robust data science tools tailored for MeRIP-Seq. Using exomePeak2, users can perform peak calling, modification site quantification and differential analysis through a straightforward single-step function. Alternatively, multi-step functions can be used to generate diagnostic plots and perform customized analyses.

package bioconductor-exomepeak2

(downloads) docker_bioconductor-exomepeak2

Versions

1.6.0-01.4.0-01.2.0-11.2.0-01.0.0-0

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>)

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