Package Recipe 'bioconductor-degcre'

recipe bioconductor-degcre

Probabilistic association of DEGs to CREs from differential data

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/DegCre.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-degcre/meta.yaml

DegCre generates associations between differentially expressed genes (DEGs) and cis-regulatory elements (CREs) based on non-parametric concordance between differential data. The user provides GRanges of DEG TSS and CRE regions with differential p-value and optionally log-fold changes and DegCre returns an annotated Hits object with associations and their calculated probabilities. Additionally, the package provides functionality for visualization and conversion to other formats.

package bioconductor-degcre¶

Versions:

1.6.0-0, 1.2.0-0

Depends:

on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-interactionset >=1.38.0,<1.39.0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-org.hs.eg.db >=3.22.0,<3.23.0
on bioconductor-plotgardener >=1.16.0,<1.17.0
on bioconductor-qvalue >=2.42.0,<2.43.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-seqinfo >=1.0.0,<1.1.0
on bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.22.0,<3.23.0
on r-base >=4.5,<4.6.0a0

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-degcre

to add into an existing workspace instead, run:

pixi add bioconductor-degcre

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-degcre

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-degcre

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-degcre:<tag>

(see bioconductor-degcre/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-degcre/README.html)