recipe bioconductor-tfbstools

TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/TFBSTools.html

License

GPL-2

Recipe

/bioconductor-tfbstools/meta.yaml

Links

biotools: tfbstools

package bioconductor-tfbstools

Versions

1.20.0-1, 1.20.0-0, 1.18.0-0, 1.16.0-0, 1.15.7-0, 1.14.2-0, 1.12.2-0

Depends

• bioconductor-biobase >=2.42.0,<2.43.0

• bioconductor-biocgenerics >=0.28.0,<0.29.0

• bioconductor-biocparallel >=1.16.0,<1.17.0

• bioconductor-biostrings >=2.50.0,<2.51.0

• bioconductor-bsgenome >=1.50.0,<1.51.0

• bioconductor-cner >=1.18.0,<1.19.0

• bioconductor-dirichletmultinomial >=1.24.0,<1.25.0

• bioconductor-genomeinfodb >=1.18.0,<1.19.0

• bioconductor-genomicranges >=1.34.0,<1.35.0

• bioconductor-iranges >=2.16.0,<2.17.0

• bioconductor-rtracklayer >=1.42.0,<1.43.0

• bioconductor-s4vectors >=0.20.0,<0.21.0

• bioconductor-seqlogo >=1.48.0,<1.49.0

• bioconductor-xvector >=0.22.0,<0.23.0

• libgcc-ng >=7.3.0

• r-base >=3.5.1,<3.5.2.0a0

• r-catools >=1.17.1

• r-dbi >=0.6

• r-gtools >=3.5.0

• r-rsqlite >=1.0.0

• r-tfmpvalue >=0.0.5

• r-xml >=3.98-1.3

Required By

• bioconductor-chromvar

• bioconductor-primirtss

• bioconductor-esatac

• bioconductor-chromvar

• bioconductor-matrixrider

• bioconductor-motifmatchr

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-tfbstools

and update with:

conda update bioconductor-tfbstools

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-tfbstools:<tag>

(see bioconductor-tfbstools/tags for valid values for <tag>)

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-tfbstools/README.html)