recipe bioconductor-ihwpaper

Reproduce figures in IHW paper

Homepage:

https://bioconductor.org/packages/3.18/data/experiment/html/IHWpaper.html

License:

Artistic-2.0

Recipe:

/bioconductor-ihwpaper/meta.yaml

This package conveniently wraps all functions needed to reproduce the figures in the IHW paper (https://www.nature.com/articles/nmeth.3885) and the data analysis in https://rss.onlinelibrary.wiley.com/doi/10.1111/rssb.12411, cf. the arXiv preprint (http://arxiv.org/abs/1701.05179). Thus it is a companion package to the Bioconductor IHW package.

package bioconductor-ihwpaper

versions:

1.28.0-0,  1.26.0-1,  1.26.0-0,  1.22.0-3,  1.22.0-2,  1.22.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-1, 

1.28.0-0,  1.26.0-1,  1.26.0-0,  1.22.0-3,  1.22.0-2,  1.22.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.10.0-0

depends bioconductor-biobase:

>=2.60.0,<2.61.0

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-biocparallel:

>=1.34.0,<1.35.0

depends bioconductor-data-packages:

>=20230706

depends bioconductor-deseq2:

>=1.40.0,<1.41.0

depends bioconductor-genefilter:

>=1.82.0,<1.83.0

depends bioconductor-ihw:

>=1.28.0,<1.29.0

depends bioconductor-qvalue:

>=2.32.0,<2.33.0

depends bioconductor-summarizedexperiment:

>=1.30.0,<1.31.0

depends curl:

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-cowplot:

depends r-dplyr:

depends r-fdrtool:

depends r-ggplot2:

depends r-rcpp:

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-ihwpaper

and update with::

   mamba update bioconductor-ihwpaper

To create a new environment, run:

mamba create --name myenvname bioconductor-ihwpaper

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-ihwpaper:<tag>

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

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