RNASeqR

DOI: 10.18129/B9.bioc.RNASeqR    

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

Bioconductor version: Release (3.15)

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>

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

PDF		Reference Manual

Details

biocViews	Alignment, Clustering, DataImport, DifferentialExpression, ExperimentalDesign, FunctionalPrediction, GO, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, Infrastructure, KEGG, Normalization, Pathways, QualityControl, RNASeq, Sequencing, Software, Visualization
Version	1.14.1
In Bioconductor since	BioC 3.8 (R-3.5) (4 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
LinkingTo
Suggests	knitr, rmarkdown, png, grid, RNASeqRData
SystemRequirements	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.
Enhances
URL	https://github.com/HowardChao/RNASeqR
BugReports	https://github.com/HowardChao/RNASeqR/issues
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Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
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/
Package Downloads Report	Download Stats