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:

/bioconductor-ataccogaps/meta.yaml

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

• r-dplyr

• r-gplots

• r-gtools

• r-msigdbr

• r-stringr

• r-tidyverse

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

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