- recipe bioconductor-methylsig
MethylSig: Differential Methylation Testing for WGBS and RRBS Data
MethylSig is a package for testing for differentially methylated cytosines (DMCs) or regions (DMRs) in whole-genome bisulfite sequencing (WGBS) or reduced representation bisulfite sequencing (RRBS) experiments. MethylSig uses a beta binomial model to test for significant differences between groups of samples. Several options exist for either site-specific or sliding window tests, and variance estimation.
- package bioconductor-methylsig¶
- depends bioconductor-bsseq:
- depends bioconductor-delayedarray:
- depends bioconductor-delayedmatrixstats:
- depends bioconductor-dss:
- depends bioconductor-genomeinfodb:
- depends bioconductor-genomicranges:
- depends bioconductor-iranges:
- depends bioconductor-s4vectors:
- depends r-base:
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-methylsig and update with:: mamba update bioconductor-methylsig
To create a new environment, run:
mamba create --name myenvname bioconductor-methylsig
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-methylsig:<tag> (see `bioconductor-methylsig/tags`_ for valid values for ``<tag>``)