- recipe bioconductor-medips
DNA IP-seq data analysis
MEDIPS was developed for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, MEDIPS provides functionalities for the analysis of any kind of quantitative sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others) including calculation of differential coverage between groups of samples and saturation and correlation analysis.
- package bioconductor-medips¶
- depends bioconductor-biomart:
- depends bioconductor-biostrings:
- depends bioconductor-bsgenome:
- depends bioconductor-dnacopy:
- depends bioconductor-edger:
- depends bioconductor-genomicranges:
- depends bioconductor-iranges:
- depends bioconductor-preprocesscore:
- depends bioconductor-rsamtools:
- depends bioconductor-rtracklayer:
- depends r-base:
- depends r-gtools:
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-medips and update with:: mamba update bioconductor-medips
To create a new environment, run:
mamba create --name myenvname bioconductor-medips
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-medips:<tag> (see `bioconductor-medips/tags`_ for valid values for ``<tag>``)