recipe bioconductor-mitch

Multi-Contrast Gene Set Enrichment Analysis

Homepage:

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

License:

CC BY-SA 4.0 + file LICENSE

Recipe:

/bioconductor-mitch/meta.yaml

mitch is an R package for multi-contrast enrichment analysis. At it’s heart, it uses a rank-MANOVA based statistical approach to detect sets of genes that exhibit enrichment in the multidimensional space as compared to the background. The rank-MANOVA concept dates to work by Cox and Mann (https://doi.org/10.1186/1471-2105-13-S16-S12). mitch is useful for pathway analysis of profiling studies with one, two or more contrasts, or in studies with multiple omics profiling, for example proteomic, transcriptomic, epigenomic analysis of the same samples. mitch is perfectly suited for pathway level differential analysis of scRNA-seq data. The main strengths of mitch are that it can import datasets easily from many upstream tools and has advanced plotting features to visualise these enrichments.

package bioconductor-mitch

versions:

1.14.0-0,  1.12.0-0,  1.10.0-0,  1.6.0-0,  1.4.0-0,  1.2.2-0,  1.2.0-0,  1.0.0-0

depends r-base:

>=4.3,<4.4.0a0

depends r-beeswarm:

depends r-echarts4r:

depends r-ggally:

depends r-ggplot2:

depends r-gplots:

depends r-gridextra:

depends r-kableextra:

depends r-knitr:

depends r-mass:

depends r-plyr:

depends r-reshape2:

depends r-rmarkdown:

requirements:

additional platforms:

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-mitch

and update with::

   mamba update bioconductor-mitch

To create a new environment, run:

mamba create --name myenvname bioconductor-mitch

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-mitch:<tag>

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

Download stats

Link to this page

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