RNASeqR

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.16 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see RNASeqRData.

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

DOI: 10.18129/B9.bioc.RNASeqR

Bioconductor version: 3.16

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.

Author: Kuan-Hao Chao

Maintainer: Kuan-Hao Chao <ntueeb05howard at gmail.com>

Citation (from within R, enter citation("RNASeqR")):

Installation

To install this package, start R (version "4.2") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("RNASeqR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("RNASeqR")

RNA-Seq analysis based on one independent variable HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

Version 1.16.0

In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)

License Artistic-2.0

Depends R (>= 3.5.0), ggplot2, pathview, edgeR, methods

Imports Rsamtools, tools, reticulate, ballgown, gridExtra, rafalib, FactoMineR, factoextra, corrplot, PerformanceAnalytics, reshape2, DESeq2, systemPipeR, systemPipeRdata, clusterProfiler, org.Hs.eg.db, org.Sc.sgd.db, stringr, pheatmap, grDevices, graphics, stats, utils, DOSE, Biostrings, parallel

System Requirements RNASeqR only support Linux and macOS. Window is not supported. Python2 is highly recommended. If your machine is Python3, make sure '2to3' command is available.

URL https://github.com/HowardChao/RNASeqR

Bug Reports https://github.com/HowardChao/RNASeqR/issues

Suggests knitr, rmarkdown, png, grid, RNASeqRData

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package RNASeqR_1.16.0.tar.gz

Windows Binary

macOS Binary (x86_64) RNASeqR_1.15.1.tgz

macOS Binary (arm64) RNASeqR_1.16.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/RNASeqR

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RNASeqR

Package Short Url https://bioconductor.org/packages/RNASeqR/

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Old Source Packages for BioC 3.16 Source Archive