RNASeqR

DOI: 10.18129/B9.bioc.RNASeqR    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see RNASeqR.

RNASeqR: RNA-Seq workflow for case-control study

Bioconductor version: 3.8

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 "3.5") and enter:

if (!requireNamespace("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")

 

HTML	R Script	RNA-Seq analysis based on one independent variable
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, Clustering, DataImport, DifferentialExpression, ExperimentalDesign, FunctionalPrediction, GO, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, Infrastructure, KEGG, Normalization, Pathways, QualityControl, RNASeq, Sequencing, Software, Visualization
Version	1.0.3
In Bioconductor since	BioC 3.8 (R-3.5) (0.5 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
LinkingTo
Suggests	knitr, 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
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	RNASeqR_1.0.3.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)	RNASeqR_1.0.3.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	http://bioconductor.org/packages/RNASeqR/
Package Downloads Report	Download Stats