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

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

(downloads) docker_bioconductor-tfbstools

versions:
1.40.0-01.38.0-01.36.0-11.36.0-01.32.0-21.32.0-11.32.0-01.30.0-01.28.0-1

1.40.0-01.38.0-01.36.0-11.36.0-01.32.0-21.32.0-11.32.0-01.30.0-01.28.0-11.28.0-01.26.0-01.24.0-01.22.0-11.20.0-11.20.0-01.18.0-01.16.0-01.15.7-01.14.2-01.12.2-0

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 myenvname being 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>``)

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