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DESCRIPTION
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DESCRIPTION
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Package: RNASeqR
Type: Package
Title: RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
Version: 1.15.1
Date: 2018-8-7
Author: Kuan-Hao Chao
Maintainer: Kuan-Hao Chao <ntueeb05howard@gmail.com>
biocViews: Genetics, Infrastructure, DataImport, Sequencing, RNASeq,
GeneExpression, GeneSetEnrichment, Alignment, QualityControl,
DifferentialExpression, FunctionalPrediction, ExperimentalDesign,
GO, KEGG, Visualization, Normalization, Pathways, Clustering,
ImmunoOncology
Description: 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.
License: Artistic-2.0
Encoding: UTF-8
RoxygenNote: 6.1.1
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,
rmarkdown,
png,
grid,
RNASeqRData
VignetteBuilder:
knitr
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.
BugReports:
https://github.com/HowardChao/RNASeqR/issues
URL:
https://github.com/HowardChao/RNASeqR
NeedsCompilation:
no