recipe bioconductor-exomepeak2

Bias-aware Peak Calling and Quantification for MeRIP-Seq

Homepage

https://bioconductor.org/packages/3.13/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

Versions

1.4.0-0,  1.2.0-1,  1.2.0-0,  1.0.0-0

Depends

• bioconductor-apeglm >=1.14.0,<1.15.0

• bioconductor-biobase >=2.52.0,<2.53.0

• bioconductor-biocgenerics >=0.38.0,<0.39.0

• bioconductor-biocparallel >=1.26.0,<1.27.0

• bioconductor-biostrings >=2.60.0,<2.61.0

• bioconductor-bsgenome >=1.60.0,<1.61.0

• bioconductor-cqn >=1.38.0,<1.39.0

• bioconductor-deseq2 >=1.32.0,<1.33.0

• bioconductor-genefilter >=1.74.0,<1.75.0

• bioconductor-genomeinfodb >=1.28.0,<1.29.0

• bioconductor-genomicalignments >=1.28.0,<1.29.0

• bioconductor-genomicfeatures >=1.44.0,<1.45.0

• bioconductor-genomicranges >=1.44.0,<1.45.0

• bioconductor-iranges >=2.26.0,<2.27.0

• bioconductor-rsamtools >=2.8.0,<2.9.0

• bioconductor-rtracklayer >=1.52.0,<1.53.0

• bioconductor-s4vectors >=0.30.0,<0.31.0

• bioconductor-summarizedexperiment >=1.22.0,<1.23.0

• r-base >=4.1,<4.2.0a0

• r-ggplot2

• r-mclust

• r-reshape2

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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