recipe bioconductor-atacseqtfea

Transcription Factor Enrichment Analysis for ATAC-seq

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-atacseqtfea/meta.yaml

Assay for Transpose-Accessible Chromatin using sequencing (ATAC-seq) is a technique to assess genome-wide chromatin accessibility by probing open chromatin with hyperactive mutant Tn5 Transposase that inserts sequencing adapters into open regions of the genome. ATACseqTFEA is an improvement of the current computational method that detects differential activity of transcription factors (TFs). ATACseqTFEA not only uses the difference of open region information, but also (or emphasizes) the difference of TFs footprints (cutting sites or insertion sites). ATACseqTFEA provides an easy, rigorous way to broadly assess TF activity changes between two conditions.

package bioconductor-atacseqtfea

Versions:

1.0.1-0

Depends:

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicalignments >=1.34.0,<1.35.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-limma >=3.54.0,<3.55.0

• bioconductor-motifmatchr >=1.20.0,<1.21.0

• bioconductor-rsamtools >=2.14.0,<2.15.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• bioconductor-tfbstools >=1.36.0,<1.37.0

• r-base >=4.2,<4.3.0a0

• r-dplyr

• r-ggplot2

• r-ggrepel

• r-matrix

• r-pracma

Required By:

Installation

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

conda install bioconductor-atacseqtfea

and update with:

conda update bioconductor-atacseqtfea

or use the docker container:

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

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

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