- 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
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
1.6.0-0
,1.4.0-0
,1.2.0-1
,1.2.0-0
,1.0.0-0
- Depends
bioconductor-apeglm
>=1.16.0,<1.17.0
bioconductor-biobase
>=2.54.0,<2.55.0
bioconductor-biocgenerics
>=0.40.0,<0.41.0
bioconductor-biocparallel
>=1.28.0,<1.29.0
bioconductor-biostrings
>=2.62.0,<2.63.0
bioconductor-bsgenome
>=1.62.0,<1.63.0
bioconductor-cqn
>=1.40.0,<1.41.0
bioconductor-deseq2
>=1.34.0,<1.35.0
bioconductor-genefilter
>=1.76.0,<1.77.0
bioconductor-genomeinfodb
>=1.30.0,<1.31.0
bioconductor-genomicalignments
>=1.30.0,<1.31.0
bioconductor-genomicfeatures
>=1.46.0,<1.47.0
bioconductor-genomicranges
>=1.46.0,<1.47.0
bioconductor-iranges
>=2.28.0,<2.29.0
bioconductor-rsamtools
>=2.10.0,<2.11.0
bioconductor-rtracklayer
>=1.54.0,<1.55.0
bioconductor-s4vectors
>=0.32.0,<0.33.0
bioconductor-summarizedexperiment
>=1.24.0,<1.25.0
r-base
>=4.1,<4.2.0a0
- 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>
)
Download stats¶
Link to this page¶
Render an badge with the following MarkDown:
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