recipe bioconductor-enrichtf

Transcription Factors Enrichment Analysis

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/enrichTF.html

License:

GPL-3

Recipe:

/bioconductor-enrichtf/meta.yaml

As transcription factors (TFs) play a crucial role in regulating the transcription process through binding on the genome alone or in a combinatorial manner, TF enrichment analysis is an efficient and important procedure to locate the candidate functional TFs from a set of experimentally defined regulatory regions. While it is commonly accepted that structurally related TFs may have similar binding preference to sequences (i.e. motifs) and one TF may have multiple motifs, TF enrichment analysis is much more challenging than motif enrichment analysis. Here we present a R package for TF enrichment analysis which combine motif enrichment with the PECA model.

package bioconductor-enrichtf

Versions:

1.14.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.6.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-1

Depends:

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-bsgenome >=1.66.0,<1.67.0

• bioconductor-clusterprofiler >=4.6.0,<4.7.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-jaspar2018 >=1.1.0,<1.2.0

• bioconductor-motifmatchr >=1.20.0,<1.21.0

• bioconductor-pipeframe >=1.14.0,<1.15.0

• bioconductor-rtracklayer >=1.58.0,<1.59.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-tfbstools >=1.36.0,<1.37.0

• r-base >=4.2,<4.3.0a0

• r-ggplot2

• r-ggpubr

• r-heatmap3

• r-magrittr

• r-r.utils

• r-rmarkdown

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-enrichtf

and update with:

conda update bioconductor-enrichtf

or use the docker container:

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

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

Download stats

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