recipe bioconductor-rnaseqr

RNASeqR: an R package for automated two-group RNA-Seq analysis workflow

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/RNASeqR.html

License:

Artistic-2.0

Recipe:

/bioconductor-rnaseqr/meta.yaml

This R package is designed for case-control RNA-Seq analysis (two-group). There are six steps: "RNASeqRParam S4 Object Creation", "Environment Setup", "Quality Assessment", "Reads Alignment & Quantification", "Gene-level Differential Analyses" and "Functional Analyses". Each step corresponds to a function in this package. After running functions in order, a basic RNASeq analysis would be done easily.

package bioconductor-rnaseqr

Versions:

1.15.1-1,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.2.1-0,  1.0.3-0

Depends:

• bioconductor-ballgown >=2.30.0,<2.31.0

• bioconductor-biostrings >=2.66.0,<2.67.0

• bioconductor-clusterprofiler >=4.6.0,<4.7.0

• bioconductor-deseq2 >=1.38.0,<1.39.0

• bioconductor-dose >=3.24.0,<3.25.0

• bioconductor-edger >=3.40.0,<3.41.0

• bioconductor-org.hs.eg.db >=3.16.0,<3.17.0

• bioconductor-org.sc.sgd.db >=3.16.0,<3.17.0

• bioconductor-pathview >=1.38.0,<1.39.0

• bioconductor-rsamtools >=2.14.0,<2.15.0

• bioconductor-systempiper >=2.4.0,<2.5.0

• bioconductor-systempiperdata >=2.2.0,<2.3.0

• r-base >=4.2,<4.3.0a0

• r-corrplot

• r-factoextra

• r-factominer

• r-ggplot2

• r-gridextra

• r-performanceanalytics

• r-pheatmap

• r-rafalib

• r-reshape2

• r-reticulate

• r-stringr

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-rnaseqr

and update with:

conda update bioconductor-rnaseqr

or use the docker container:

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

(see bioconductor-rnaseqr/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-rnaseqr/README.html)