- recipe bioconductor-cssq
Chip-seq Signal Quantifier Pipeline
This package is desgined to perform statistical analysis to identify statistically significant differentially bound regions between multiple groups of ChIP-seq dataset.
- package bioconductor-cssq¶
- depends bioconductor-genomicalignments:
- depends bioconductor-genomicfeatures:
- depends bioconductor-genomicranges:
- depends bioconductor-iranges:
- depends bioconductor-rsamtools:
- depends bioconductor-rtracklayer:
- depends bioconductor-s4vectors:
- depends bioconductor-summarizedexperiment:
- depends r-base:
- depends r-ggplot2:
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-cssq and update with:: mamba update bioconductor-cssq
To create a new environment, run:
mamba create --name myenvname bioconductor-cssq
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-cssq:<tag> (see `bioconductor-cssq/tags`_ for valid values for ``<tag>``)