-
recipe
bioconductor-exomepeak2
Bias Awared Peak Calling and Quantification for MeRIP-Seq
- Homepage
https://bioconductor.org/packages/3.12/bioc/html/exomePeak2.html
- License
GPL (>= 2)
- Recipe
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
1.2.0-0
,1.0.0-0
- Depends
bioconductor-apeglm
>=1.12.0,<1.13.0
bioconductor-biobase
>=2.50.0,<2.51.0
bioconductor-biocparallel
>=1.24.0,<1.25.0
bioconductor-biostrings
>=2.58.0,<2.59.0
bioconductor-bsgenome
>=1.58.0,<1.59.0
bioconductor-cqn
>=1.36.0,<1.37.0
bioconductor-deseq2
>=1.30.0,<1.31.0
bioconductor-genefilter
>=1.72.0,<1.73.0
bioconductor-genomeinfodb
>=1.26.0,<1.27.0
bioconductor-genomicalignments
>=1.26.0,<1.27.0
bioconductor-genomicfeatures
>=1.42.0,<1.43.0
bioconductor-genomicranges
>=1.42.0,<1.43.0
bioconductor-iranges
>=2.24.0,<2.25.0
bioconductor-rsamtools
>=2.6.0,<2.7.0
bioconductor-rtracklayer
>=1.50.0,<1.51.0
bioconductor-s4vectors
>=0.28.0,<0.29.0
bioconductor-summarizedexperiment
>=1.20.0,<1.21.0
r-base
>=4.0,<4.1.0a0
- 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>
)
Link to this page¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-exomepeak2/README.html)