recipe bioconductor-tfbstools

Software Package for Transcription Factor Binding Site (TFBS) Analysis

Homepage:

https://bioconductor.org/packages/3.14/bioc/html/TFBSTools.html

License:

GPL-2

Recipe:

/bioconductor-tfbstools/meta.yaml

Links:

biotools: 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.

package bioconductor-tfbstools

Versions:

1.32.0-2,  1.32.0-1,  1.32.0-0,  1.30.0-0,  1.28.0-1,  1.28.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-1, 

1.32.0-2,  1.32.0-1,  1.32.0-0,  1.30.0-0,  1.28.0-1,  1.28.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-1,  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 >=2.54.0,<2.55.0

• bioconductor-biocgenerics >=0.40.0,<0.41.0

• bioconductor-biocparallel >=1.28.0,<1.29.0

• bioconductor-biostrings >=2.62.0,<2.63.0

• bioconductor-bsgenome >=1.62.0,<1.63.0

• bioconductor-cner >=1.30.0,<1.31.0

• bioconductor-dirichletmultinomial >=1.36.0,<1.37.0

• bioconductor-genomeinfodb >=1.30.0,<1.31.0

• bioconductor-genomicranges >=1.46.0,<1.47.0

• bioconductor-iranges >=2.28.0,<2.29.0

• bioconductor-rtracklayer >=1.54.0,<1.55.0

• bioconductor-s4vectors >=0.32.0,<0.33.0

• bioconductor-seqlogo >=1.60.0,<1.61.0

• bioconductor-xvector >=0.34.0,<0.35.0

• libblas >=3.9.0,<4.0a0

• libgcc-ng >=12

• liblapack >=3.9.0,<4.0a0

• r-base >=4.1,<4.2.0a0

• 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-monalisa

• bioconductor-primirtss

• bioconductor-enrichtf

• bioconductor-spatzie

• bioconductor-esatac

• bioconductor-motifmatchr

• bioconductor-matrixrider

Installation

With an activated Bioconda channel (see 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>)

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