- recipe bioconductor-ataccogaps
Analysis Tools for scATACseq Data with CoGAPS
- Homepage:
https://bioconductor.org/packages/3.16/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:
1.0.0-0
- Depends:
bioconductor-bsgenome.hsapiens.ucsc.hg19
>=1.4.0,<1.5.0
bioconductor-bsgenome.mmusculus.ucsc.mm10
>=1.4.0,<1.5.0
bioconductor-chromvar
>=1.20.0,<1.21.0
bioconductor-cogaps
>=3.18.0,<3.19.0
bioconductor-fgsea
>=1.24.0,<1.25.0
bioconductor-geneoverlap
>=1.34.0,<1.35.0
bioconductor-genomicfeatures
>=1.50.0,<1.51.0
bioconductor-genomicranges
>=1.50.0,<1.51.0
bioconductor-homo.sapiens
>=1.3.0,<1.4.0
bioconductor-iranges
>=2.32.0,<2.33.0
bioconductor-jaspar2016
>=1.26.0,<1.27.0
bioconductor-motifmatchr
>=1.20.0,<1.21.0
bioconductor-mus.musculus
>=1.3.0,<1.4.0
bioconductor-projectr
>=1.14.0,<1.15.0
bioconductor-rgreat
>=2.0.0,<2.1.0
bioconductor-tfbstools
>=1.36.0,<1.37.0
r-base
>=4.2,<4.3.0a0
- Required By:
Installation
With an activated Bioconda channel (see set-up-channels), install with:
conda install bioconductor-ataccogaps
and update with:
conda update bioconductor-ataccogaps
or 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)