recipe bioconductor-ballgown

Flexible, isoform-level differential expression analysis

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/ballgown.html

License:

Artistic-2.0

Recipe:

/bioconductor-ballgown/meta.yaml

Links:

biotools: ballgown, doi: 10.1038/nbt.3172

Tools for statistical analysis of assembled transcriptomes, including flexible differential expression analysis, visualization of transcript structures, and matching of assembled transcripts to annotation.

package bioconductor-ballgown

versions:

2.32.0-0,  2.30.0-0,  2.26.0-0,  2.24.0-0,  2.22.0-1,  2.22.0-0,  2.20.0-0,  2.18.0-0,  2.16.0-1, 

2.32.0-0,  2.30.0-0,  2.26.0-0,  2.24.0-0,  2.22.0-1,  2.22.0-0,  2.20.0-0,  2.18.0-0,  2.16.0-1,  2.14.0-0,  2.12.0-0,  2.10.0-0,  2.8.4-0,  2.2.0-0

depends bioconductor-biobase:

>=2.60.0,<2.61.0

depends bioconductor-genomeinfodb:

>=1.36.0,<1.37.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-limma:

>=3.56.0,<3.57.0

depends bioconductor-rtracklayer:

>=1.60.0,<1.61.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends bioconductor-sva:

>=3.48.0,<3.49.0

depends r-base:

>=4.3,<4.4.0a0

depends r-rcolorbrewer:

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-ballgown

and update with::

   mamba update bioconductor-ballgown

To create a new environment, run:

mamba create --name myenvname bioconductor-ballgown

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-ballgown:<tag>

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