Package Recipe 'bioconductor-atacseqtfea'

recipe bioconductor-atacseqtfea

Transcription Factor Enrichment Analysis for ATAC-seq

Homepage:: https://bioconductor.org/packages/3.20/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:

1.12.0-0, 1.8.0-0, 1.4.0-0, 1.2.0-0, 1.0.1-0

Depends:

on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-genomicalignments >=1.46.0,<1.47.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-motifmatchr >=1.32.0,<1.33.0
on bioconductor-rsamtools >=2.26.0,<2.27.0
on bioconductor-rtracklayer >=1.70.0,<1.71.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-seqinfo >=1.0.0,<1.1.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on bioconductor-tfbstools >=1.48.0,<1.49.0
on r-base >=4.5,<4.6.0a0
on r-dplyr
on r-ggplot2
on r-ggrepel
on r-matrix
on r-pracma

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-atacseqtfea

to add into an existing workspace instead, run:

pixi add bioconductor-atacseqtfea

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-atacseqtfea

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-atacseqtfea

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-atacseqtfea/README.html)