recipe ssdrippipeline

Useful tools for the analysis of ssDRIP-seq data







package ssdrippipeline

(downloads) docker_ssdrippipeline



depends bedtools:


depends bioconductor-deseq2:


depends bioconductor-mfuzz:


depends biopython:


depends bowtie2:


depends deeptools:


depends homer:


depends macs2:


depends matplotlib-base:


depends numpy:


depends pandas:


depends picard:


depends python:


depends r-base:


depends r-gplots:


depends samtools:


depends scipy:


depends seaborn:


depends ucsc-bedgraphtobigwig:



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 ssdrippipeline

and update with::

   mamba update ssdrippipeline

To create a new environment, run:

mamba create --name myenvname ssdrippipeline

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `ssdrippipeline/tags`_ for valid values for ``<tag>``)

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