- recipe bioconductor-exomepeak2
Peak Calling and differential analysis for MeRIP-Seq
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/exomePeak2.html
- License:
Artistic-2.0
- Recipe:
exomePeak2 provides peak detection and differential methylation for Methylated RNA Immunoprecipitation Sequencing (MeRIP-Seq) data. MeRIP-Seq is a commonly applied sequencing assay that measures the location and abundance of RNA modification sites under specific cellular conditions. The technique is sensitive to PCR amplification biases commonly found in NGS data. In addition, the efficiency of immunoprecipitation often varies between different IP samples. exomePeak2 can perform peak calling and differential analysis independent of GC content bias and IP efficiency changes.
- package bioconductor-exomepeak2¶
- versions:
1.14.3-0,1.12.0-0,1.10.0-0,1.6.0-0,1.4.0-0,1.2.0-1,1.2.0-0,1.0.0-0- depends bioconductor-biocgenerics:
>=0.48.0,<0.49.0- depends bioconductor-biocparallel:
>=1.36.0,<1.37.0- depends bioconductor-biostrings:
>=2.70.0,<2.71.0- depends bioconductor-bsgenome:
>=1.70.0,<1.71.0- depends bioconductor-deseq2:
>=1.42.0,<1.43.0- depends bioconductor-genomeinfodb:
>=1.38.0,<1.39.0- depends bioconductor-genomicalignments:
>=1.38.0,<1.39.0- depends bioconductor-genomicfeatures:
>=1.54.0,<1.55.0- depends bioconductor-genomicranges:
>=1.54.0,<1.55.0- depends bioconductor-iranges:
>=2.36.0,<2.37.0- depends bioconductor-rsamtools:
>=2.18.0,<2.19.0- depends bioconductor-rtracklayer:
>=1.62.0,<1.63.0- depends bioconductor-s4vectors:
>=0.40.0,<0.41.0- depends bioconductor-summarizedexperiment:
>=1.32.0,<1.33.0- depends r-base:
>=4.3,<4.4.0a0- depends r-ggplot2:
- depends r-magrittr:
- depends r-mclust:
- depends r-speedglm:
- requirements:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bioconductor-exomepeak2 and update with:: mamba update bioconductor-exomepeak2
To create a new environment, run:
mamba create --name myenvname bioconductor-exomepeak2
with
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, 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:
[](http://bioconda.github.io/recipes/bioconductor-exomepeak2/README.html)
