recipe bioconductor-rnaseqr

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.

Homepage

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

License

Artistic-2.0

Recipe

/bioconductor-rnaseqr/meta.yaml

package bioconductor-rnaseqr

(downloads) docker_bioconductor-rnaseqr

Versions

1.0.3-0

Depends bioconductor-ballgown

>=2.14.0,<2.15.0

Depends bioconductor-biostrings

>=2.50.0,<2.51.0

Depends bioconductor-clusterprofiler

>=3.10.0,<3.11.0

Depends bioconductor-deseq2

>=1.22.0,<1.23.0

Depends bioconductor-dose

>=3.8.0,<3.9.0

Depends bioconductor-edger

>=3.24.0,<3.25.0

Depends bioconductor-org.hs.eg.db

>=3.7.0,<3.8.0

Depends bioconductor-org.sc.sgd.db

>=3.7.0,<3.8.0

Depends bioconductor-pathview

>=1.22.0,<1.23.0

Depends bioconductor-rsamtools

>=1.34.0,<1.35.0

Depends bioconductor-systempiper

>=1.16.0,<1.17.0

Depends bioconductor-systempiperdata

>=1.10.0,<1.11.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-corrplot

Depends r-factoextra

Depends r-factominer

Depends r-ggplot2

Depends r-gridextra

Depends r-performanceanalytics

Depends r-pheatmap

Depends r-rafalib

Depends r-reshape2

Depends r-reticulate

Depends r-stringr

Requirements

Installation

With an activated Bioconda channel (see 2. 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>)