- recipe bioconductor-ataccogaps
Analysis Tools for scATACseq Data with CoGAPS
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/ATACCoGAPS.html
- License:
Artistic-2.0
- Recipe:
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¶
- versions:
1.4.0-0,1.2.0-0,1.0.0-0- depends bioconductor-bsgenome.hsapiens.ucsc.hg19:
>=1.4.0,<1.5.0- depends bioconductor-bsgenome.mmusculus.ucsc.mm10:
>=1.4.0,<1.5.0- depends bioconductor-chromvar:
>=1.24.0,<1.25.0- depends bioconductor-cogaps:
>=3.22.0,<3.23.0- depends bioconductor-fgsea:
>=1.28.0,<1.29.0- depends bioconductor-geneoverlap:
>=1.38.0,<1.39.0- depends bioconductor-genomicfeatures:
>=1.54.0,<1.55.0- depends bioconductor-genomicranges:
>=1.54.0,<1.55.0- depends bioconductor-homo.sapiens:
>=1.3.0,<1.4.0- depends bioconductor-iranges:
>=2.36.0,<2.37.0- depends bioconductor-jaspar2016:
>=1.30.0,<1.31.0- depends bioconductor-motifmatchr:
>=1.24.0,<1.25.0- depends bioconductor-mus.musculus:
>=1.3.0,<1.4.0- depends bioconductor-projectr:
>=1.18.0,<1.19.0- depends bioconductor-rgreat:
>=2.4.0,<2.5.0- depends bioconductor-tfbstools:
>=1.40.0,<1.41.0- depends r-base:
>=4.3,<4.4.0a0- depends r-dplyr:
- depends r-gplots:
- depends r-gtools:
- depends r-msigdbr:
- depends r-stringr:
- depends r-tidyverse:
- requirements:
Installation
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
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-ataccogaps:<tag> (see `bioconductor-ataccogaps/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-ataccogaps/README.html)
