recipe bioconductor-ssnappy

Single Sample directioNAl Pathway Perturbation analYsis

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-ssnappy/meta.yaml

A single sample pathway perturbation testing method for RNA-seq data. The method propagates changes in gene expression down gene-set topologies to compute single-sample directional pathway perturbation scores that reflect potential direction of change. Perturbation scores can be used to test significance of pathway perturbation at both individual-sample and treatment levels.

package bioconductor-ssnappy

versions:

1.6.1-0,  1.4.1-0,  1.2.0-1,  1.2.0-0

depends bioconductor-edger:

>=4.0.0,<4.1.0

depends bioconductor-graphite:

>=1.48.0,<1.49.0

depends bioconductor-org.hs.eg.db:

>=3.18.0,<3.19.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

>=1.1

depends r-ggforce:

depends r-ggplot2:

depends r-ggraph:

depends r-gtools:

depends r-igraph:

depends r-magrittr:

depends r-pheatmap:

depends r-reshape2:

depends r-rlang:

depends r-stringr:

depends r-tibble:

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-ssnappy

and update with::

   mamba update bioconductor-ssnappy

To create a new environment, run:

mamba create --name myenvname bioconductor-ssnappy

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-ssnappy:<tag>

(see `bioconductor-ssnappy/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-ssnappy/README.html)