recipe bioconductor-atacseqtfea

Transcription Factor Enrichment Analysis for ATAC-seq

Homepage:

https://bioconductor.org/packages/3.18/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:

1.4.0-0,  1.2.0-0,  1.0.1-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicalignments:

>=1.38.0,<1.39.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-motifmatchr:

>=1.24.0,<1.25.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-tfbstools:

>=1.40.0,<1.41.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-ggplot2:

depends r-ggrepel:

depends r-matrix:

depends r-pracma:

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-atacseqtfea

and update with::

   mamba update bioconductor-atacseqtfea

To create a new environment, run:

mamba create --name myenvname bioconductor-atacseqtfea

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-atacseqtfea:<tag>

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

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