recipe bioconductor-ataccogaps

Analysis Tools for scATACseq Data with CoGAPS






Provides tools for running the CoGAPS algorithm (Fertig et al, 2010) on single-cell ATAC sequencing data and analysis of the results. Can be used to perform analyses at the level of genes, motifs, TFs, or pathways. Additionally provides tools for transfer learning and data integration with single-cell RNA sequencing data.

package bioconductor-ataccogaps

(downloads) docker_bioconductor-ataccogaps



depends bioconductor-bsgenome.hsapiens.ucsc.hg19:


depends bioconductor-bsgenome.mmusculus.ucsc.mm10:


depends bioconductor-chromvar:


depends bioconductor-cogaps:


depends bioconductor-fgsea:


depends bioconductor-geneoverlap:


depends bioconductor-genomicfeatures:


depends bioconductor-genomicranges:


depends bioconductor-homo.sapiens:


depends bioconductor-iranges:


depends bioconductor-jaspar2016:


depends bioconductor-motifmatchr:


depends bioconductor-mus.musculus:


depends bioconductor-projectr:


depends bioconductor-rgreat:


depends bioconductor-tfbstools:


depends r-base:


depends r-dplyr:

depends r-gplots:

depends r-gtools:

depends r-msigdbr:

depends r-stringr:

depends r-tidyverse:



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-ataccogaps

and update with::

   mamba update bioconductor-ataccogaps

To create a new environment, run:

mamba create --name myenvname bioconductor-ataccogaps

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 `bioconductor-ataccogaps/tags`_ for valid values for ``<tag>``)

Download stats