recipe bioconductor-degreport

Report of DEG analysis

Homepage

https://bioconductor.org/packages/3.11/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

1.24.0-0, 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 >=2.48.0,<2.49.0

• bioconductor-biocgenerics >=0.34.0,<0.35.0

• bioconductor-complexheatmap >=2.4.0,<2.5.0

• bioconductor-consensusclusterplus >=1.52.0,<1.53.0

• bioconductor-deseq2 >=1.28.0,<1.29.0

• bioconductor-edger >=3.30.0,<3.31.0

• bioconductor-s4vectors >=0.26.0,<0.27.0

• bioconductor-summarizedexperiment >=1.18.0,<1.19.0

• r-base >=4.0,<4.1.0a0

• r-broom

• r-circlize

• r-cluster

• r-cowplot

• r-dplyr

• r-ggdendro

• r-ggplot2

• r-ggrepel

• r-knitr

• r-lasso2

• r-logging

• r-magrittr

• r-nozzle.r1

• r-psych

• r-rcolorbrewer

• r-reshape

• r-rlang

• r-scales

• r-stringr

• r-tibble

• r-tidyr

Required By

• bcbio-rnaseq

• bioconductor-isomirs

• r-bcbiornaseq

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-degreport

and update with:

conda update bioconductor-degreport

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-degreport:<tag>

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

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-degreport/README.html)