recipe bioconductor-degreport

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.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/DEGreport.html

License

MIT + file LICENSE

Recipe

/bioconductor-degreport/meta.yaml

Links

biotools: degreport, doi: 10.1038/nmeth.3252

package bioconductor-degreport

(downloads) docker_bioconductor-degreport

Versions

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

Depends bioconductor-biocgenerics

Depends bioconductor-complexheatmap

Depends bioconductor-consensusclusterplus

Depends bioconductor-deseq2

Depends bioconductor-edger

Depends bioconductor-s4vectors

Depends bioconductor-summarizedexperiment

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-broom

Depends r-circlize

Depends r-cluster

Depends r-cowplot

Depends r-dplyr

Depends r-ggdendro

Depends r-ggplot2

Depends r-ggrepel

Depends r-knitr

Depends r-lasso2

Depends r-logging

Depends r-magrittr

Depends r-nozzle.r1

Depends r-psych

Depends r-rcolorbrewer

Depends r-reshape

Depends r-rlang

Depends r-scales

Depends r-stringr

Depends r-tibble

Depends r-tidyr

Requirements

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>)