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>

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


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HTML R Script RNA-Seq analysis based on one independent variable
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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
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.
URL https://github.com/HowardChao/RNASeqR
BugReports https://github.com/HowardChao/RNASeqR/issues
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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/
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