- recipe bioconductor-tfbstools
Software Package for Transcription Factor Binding Site (TFBS) Analysis
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/TFBSTools.html
- License:
GPL-2.0-only
- Recipe:
- 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:
1.40.0-1,1.40.0-0,1.38.0-0,1.36.0-1,1.36.0-0,1.32.0-2,1.32.0-1,1.32.0-0,1.30.0-0,1.40.0-1,1.40.0-0,1.38.0-0,1.36.0-1,1.36.0-0,1.32.0-2,1.32.0-1,1.32.0-0,1.30.0-0,1.28.0-1,1.28.0-0,1.26.0-0,1.24.0-0,1.22.0-1,1.20.0-1,1.20.0-0,1.18.0-0,1.16.0-0,1.15.7-0,1.14.2-0,1.12.2-0- depends bioconductor-biobase:
>=2.62.0,<2.63.0- depends bioconductor-biobase:
>=2.62.0,<2.63.0a0- depends bioconductor-biocgenerics:
>=0.48.0,<0.49.0- depends bioconductor-biocgenerics:
>=0.48.1,<0.49.0a0- depends bioconductor-biocparallel:
>=1.36.0,<1.37.0- depends bioconductor-biocparallel:
>=1.36.0,<1.37.0a0- depends bioconductor-biostrings:
>=2.70.0,<2.71.0- depends bioconductor-biostrings:
>=2.70.1,<2.71.0a0- depends bioconductor-bsgenome:
>=1.70.0,<1.71.0- depends bioconductor-bsgenome:
>=1.70.1,<1.71.0a0- depends bioconductor-cner:
>=1.38.0,<1.39.0- depends bioconductor-cner:
>=1.38.0,<1.39.0a0- depends bioconductor-dirichletmultinomial:
>=1.44.0,<1.45.0- depends bioconductor-dirichletmultinomial:
>=1.44.0,<1.45.0a0- depends bioconductor-genomeinfodb:
>=1.38.0,<1.39.0- depends bioconductor-genomeinfodb:
>=1.38.1,<1.39.0a0- depends bioconductor-genomicranges:
>=1.54.0,<1.55.0- depends bioconductor-genomicranges:
>=1.54.1,<1.55.0a0- depends bioconductor-iranges:
>=2.36.0,<2.37.0- depends bioconductor-iranges:
>=2.36.0,<2.37.0a0- depends bioconductor-rtracklayer:
>=1.62.0,<1.63.0- depends bioconductor-rtracklayer:
>=1.62.0,<1.63.0a0- depends bioconductor-s4vectors:
>=0.40.0,<0.41.0- depends bioconductor-s4vectors:
>=0.40.2,<0.41.0a0- depends bioconductor-seqlogo:
>=1.68.0,<1.69.0- depends bioconductor-seqlogo:
>=1.68.0,<1.69.0a0- depends bioconductor-xvector:
>=0.42.0,<0.43.0- depends bioconductor-xvector:
>=0.42.0,<0.43.0a0- depends libblas:
>=3.9.0,<4.0a0- depends libgcc-ng:
>=12- depends liblapack:
>=3.9.0,<4.0a0- depends r-base:
>=4.3,<4.4.0a0- depends r-catools:
>=1.17.1- depends r-dbi:
>=0.6- depends r-gtools:
>=3.5.0- depends r-rsqlite:
>=1.0.0- depends r-tfmpvalue:
>=0.0.5- depends r-xml:
>=3.98-1.3- 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-tfbstools and update with:: mamba update bioconductor-tfbstools
To create a new environment, run:
mamba create --name myenvname bioconductor-tfbstools
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-tfbstools:<tag> (see `bioconductor-tfbstools/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-tfbstools/README.html)
