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This is the development version of RNASeqR; for the stable release version, see RNASeqR.
Bioconductor version: Development (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")
):
To install this package, start R (version "4.2") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") # The following initializes usage of Bioc devel BiocManager::install(version='devel') BiocManager::install("RNASeqR")
For older versions of R, please refer to the appropriate Bioconductor release.
Reference Manual |
biocViews | Alignment, Clustering, DataImport, DifferentialExpression, ExperimentalDesign, FunctionalPrediction, GO, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, Infrastructure, KEGG, Normalization, Pathways, QualityControl, RNASeq, Sequencing, Software, Visualization |
Version | 1.15.1 |
In Bioconductor since | BioC 3.8 (R-3.5) (3.5 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, 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 |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | |
Windows Binary | |
macOS 10.13 (High Sierra) | |
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 |
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