recipe bioconductor-broadseq

broadSeq : for streamlined exploration of RNA-seq data

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/broadSeq.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-broadseq/meta.yaml

This package helps user to do easily RNA-seq data analysis with multiple methods (usually which needs many different input formats). Here the user will provid the expression data as a SummarizedExperiment object and will get results from different methods. It will help user to quickly evaluate different methods.

package bioconductor-broadseq

versions:

1.0.0-0

depends bioconductor-biocstyle:

>=2.34.0,<2.35.0

depends bioconductor-clusterprofiler:

>=4.14.0,<4.15.0

depends bioconductor-delocal:

>=1.6.0,<1.7.0

depends bioconductor-deseq2:

>=1.46.0,<1.47.0

depends bioconductor-ebseq:

>=2.4.0,<2.5.0

depends bioconductor-edger:

>=4.4.0,<4.5.0

depends bioconductor-genefilter:

>=1.88.0,<1.89.0

depends bioconductor-noiseq:

>=2.50.0,<2.51.0

depends bioconductor-sechm:

>=1.14.0,<1.15.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-base:

>=4.4,<4.5.0a0

depends r-dplyr:

depends r-forcats:

>=1.0.0

depends r-ggplot2:

depends r-ggplotify:

depends r-ggpubr:

depends r-pheatmap:

depends r-plyr:

depends r-purrr:

>=0.3.5

depends r-stringr:

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-broadseq

and update with::

   mamba update bioconductor-broadseq

To create a new environment, run:

mamba create --name myenvname bioconductor-broadseq

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-broadseq:<tag>

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