recipe bioconductor-rcistarget

RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/RcisTarget.html

License:

GPL-3

Recipe:

/bioconductor-rcistarget/meta.yaml

RcisTarget identifies transcription factor binding motifs (TFBS) over-represented on a gene list. In a first step, RcisTarget selects DNA motifs that are significantly over-represented in the surroundings of the transcription start site (TSS) of the genes in the gene-set. This is achieved by using a database that contains genome-wide cross-species rankings for each motif. The motifs that are then annotated to TFs and those that have a high Normalized Enrichment Score (NES) are retained. Finally, for each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. genes in the gene-set that are ranked above the leading edge).

package bioconductor-rcistarget

versions:

1.20.0-0,  1.17.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1, 

1.20.0-0,  1.17.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.2.1-0,  1.2.0-0

depends bioconductor-aucell:

>=1.22.0,<1.23.0

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-genomeinfodb:

>=1.36.0,<1.37.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-gseabase:

>=1.62.0,<1.63.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends bioconductor-summarizedexperiment:

>=1.30.0,<1.31.0

depends r-arrow:

>=2.0.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-dplyr:

depends r-r.utils:

depends r-tibble:

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-rcistarget

and update with::

   mamba update bioconductor-rcistarget

To create a new environment, run:

mamba create --name myenvname bioconductor-rcistarget

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-rcistarget:<tag>

(see `bioconductor-rcistarget/tags`_ for valid values for ``<tag>``)

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