recipe bioconductor-degreport

Report of DEG analysis

Homepage:

https://bioconductor.org/packages/3.16/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:

1.34.0-0,  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, 

1.34.0-0,  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 >=2.58.0,<2.59.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-complexheatmap >=2.14.0,<2.15.0

• bioconductor-consensusclusterplus >=1.62.0,<1.63.0

• bioconductor-deseq2 >=1.38.0,<1.39.0

• bioconductor-edger >=3.40.0,<3.41.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-base >=4.2,<4.3.0a0

• r-broom

• r-circlize

• r-cluster

• r-cowplot

• r-dplyr

• r-ggdendro

• r-ggplot2

• r-ggrepel

• r-knitr

• r-logging

• r-magrittr

• r-psych

• r-rcolorbrewer

• r-reshape

• r-rlang

• r-scales

• r-stringr

• r-tibble

• r-tidyr

Required By:

• bioconductor-isomirs

• bcbio-rnaseq

• r-bcbiornaseq

Installation

With an activated Bioconda channel (see 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>)

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-degreport/README.html)