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

Versions

1.0.0-0

Depends

• bioconductor-apeglm >=1.10.0,<1.11.0

• bioconductor-biobase >=2.48.0,<2.49.0

• bioconductor-biocparallel >=1.22.0,<1.23.0

• bioconductor-biostrings >=2.56.0,<2.57.0

• bioconductor-bsgenome >=1.56.0,<1.57.0

• bioconductor-cqn >=1.34.0,<1.35.0

• bioconductor-deseq2 >=1.28.0,<1.29.0

• bioconductor-genefilter >=1.70.0,<1.71.0

• bioconductor-genomeinfodb >=1.24.0,<1.25.0

• bioconductor-genomicalignments >=1.24.0,<1.25.0

• bioconductor-genomicfeatures >=1.40.0,<1.41.0

• bioconductor-genomicranges >=1.40.0,<1.41.0

• bioconductor-iranges >=2.22.0,<2.23.0

• bioconductor-rsamtools >=2.4.0,<2.5.0

• bioconductor-rtracklayer >=1.48.0,<1.49.0

• bioconductor-s4vectors >=0.26.0,<0.27.0

• bioconductor-summarizedexperiment >=1.18.0,<1.19.0

• r-base >=4.0,<4.1.0a0

• r-ggplot2

• r-mclust

• r-reshape2

• r-rmariadb

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>)

Link to this page

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