recipe bioconductor-tadcompare

TADCompare: Identification and characterization of differential TADs

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/TADCompare.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-tadcompare/meta.yaml

TADCompare is an R package designed to identify and characterize differential Topologically Associated Domains (TADs) between multiple Hi-C contact matrices. It contains functions for finding differential TADs between two datasets, finding differential TADs over time and identifying consensus TADs across multiple matrices. It takes all of the main types of HiC input and returns simple, comprehensive, easy to analyze results.

package bioconductor-tadcompare

versions:

1.12.0-0,  1.10.0-0,  1.8.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-1,  1.0.0-0

depends bioconductor-hiccompare:

>=1.24.0,<1.25.0

depends r-base:

>=4.3,<4.4.0a0

depends r-cluster:

depends r-cowplot:

depends r-dplyr:

depends r-ggplot2:

depends r-ggpubr:

depends r-magrittr:

depends r-matrix:

depends r-primme:

depends r-rcolorbrewer:

depends r-reshape2:

depends r-tidyr:

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-tadcompare

and update with::

   mamba update bioconductor-tadcompare

To create a new environment, run:

mamba create --name myenvname bioconductor-tadcompare

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-tadcompare:<tag>

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

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-tadcompare/README.html)