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
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("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 | ||
| NEWS | Text |
Details
| biocViews | Alignment, Clustering, DataImport, DifferentialExpression, ExperimentalDesign, FunctionalPrediction, GO, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, Infrastructure, KEGG, Normalization, Pathways, QualityControl, RNASeq, Sequencing, Software, Visualization |
| 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 |
See More
| Suggests | knitr, rmarkdown, png, grid, RNASeqRData |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
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/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.16 | Source Archive |