recipe bioconductor-degreport

Report of DEG analysis

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-degreport/meta.yaml

Links:

biotools: degreport, doi: 10.1038/nmeth.3252

Creation of a HTML report of differential expression analyses of count data. It integrates some of the code mentioned in DESeq2 and edgeR vignettes, and report a ranked list of genes according to the fold changes mean and variability for each selected gene.

package bioconductor-degreport

versions:

1.38.4-0,  1.36.0-0,  1.34.0-0,  1.30.0-0,  1.28.0-0,  1.26.0-1,  1.26.0-0,  1.24.0-0,  1.22.0-0, 

1.38.4-0,  1.36.0-0,  1.34.0-0,  1.30.0-0,  1.28.0-0,  1.26.0-1,  1.26.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-1,  1.19.1-0,  1.18.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.8.2-1,  1.8.2-0,  1.7.2-1

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-complexheatmap:

>=2.18.0,<2.19.0

depends bioconductor-consensusclusterplus:

>=1.66.0,<1.67.0

depends bioconductor-deseq2:

>=1.42.0,<1.43.0

depends bioconductor-edger:

>=4.0.0,<4.1.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-broom:

depends r-circlize:

depends r-cluster:

depends r-cowplot:

depends r-dendextend:

depends r-dplyr:

depends r-ggdendro:

depends r-ggplot2:

depends r-ggrepel:

depends r-knitr:

depends r-logging:

depends r-magrittr:

depends r-psych:

depends r-rcolorbrewer:

depends r-reshape:

depends r-rlang:

depends r-scales:

depends r-stringi:

depends r-stringr:

depends r-tibble:

depends r-tidyr:

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-degreport

and update with::

   mamba update bioconductor-degreport

To create a new environment, run:

mamba create --name myenvname bioconductor-degreport

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-degreport:<tag>

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

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