├── .gitignore ├── Annotation └── hgu133plus2.db.R ├── AnnotationHub └── AnnotationHub.R ├── ArrayExpress └── ArrayExpress.R ├── GEO ├── Affy.R ├── CLL.R ├── DataMining1.R ├── DataMining2.R ├── GEOquery.R ├── IfLogScale.R ├── TXDB.R └── limma.R ├── GOstats └── GOstats.R ├── GenomicRange └── bedOverlap_DAEC1.r ├── KEGGprofile └── KEGGenrichment.R ├── LICENSE ├── Methylation ├── 450KMethylationpipeline └── minfi.R ├── README.md ├── RcolorBrowser ├── RColorBrewer.R ├── colortools.R ├── ggsci.R └── wesanderson.R ├── Rdownload ├── SRAdb │ ├── SRAdb.R │ └── dowload.R └── aspera.sh ├── RfileSystem └── AutoCreateDir.R ├── Rplot ├── 3.1.Diff_expression_GSE46691_plot.R ├── CombinePlot.R ├── ComplexHeatmap.R ├── GroupPlot.R ├── InteractivePlot.R ├── Volcano.R ├── addAnnotation.R ├── barplot.R ├── boxplot.R ├── bubbleplot(scatterplot).R ├── dotplot.R ├── forestplot.R ├── forestplotdata.xlsx ├── ggplot2.R ├── ggplot2.doc ├── ggstatsplot.R ├── gplots.R ├── gradientColor.R ├── maftools.R ├── pheatmap.R ├── pie.R ├── scRNAseq │ ├── Figure 1.R │ ├── Figure 2.R │ └── Figure 3.R ├── vennplot.R ├── vioplot.R └── 互斥共发生热图.r ├── RtoWord └── RtoWord.R ├── Rupdate ├── installRpackages.R └── update.R ├── Rweb ├── RCurl.R ├── RMysql.R ├── RinCMD.R ├── Rlink2DiseaseEnhancer.R ├── Rlink2MutExGenome.R └── Rvest.R ├── SingleCell ├── Explore_HCC1.R └── ICC.R ├── TCGA └── TCGAbiolinks.R ├── Trascription ├── ReadCountFromBam.R ├── Single.R └── airway.R ├── clusterProfiler └── clusterProfiler.R ├── common.R ├── doParallel └── foreach.R ├── docker.R ├── github.R ├── gsea └── gsea.R ├── igraph ├── RWR.R ├── degreeDistrPlot.R ├── igraph.R └── network.R ├── init.R ├── initBioinforR.R ├── install.R ├── org.Hs.eg.db └── org.Hs.eg.db.R ├── pkgSearch └── pkgSearch.R ├── regioneR └── regioneR.R ├── rjson └── rjson.R ├── rmarkdown ├── r.snippets ├── r_markdown_v2_presentation.Rmd └── rmarkdowm.R ├── singleCell ├── monocle.R └── seurat.R ├── software ├── .bash_profile ├── .bashrc ├── Pipelines.jsp ├── RsyncCmd_RNA.sh ├── atacCallPeak.sh ├── bash_profile.sh ├── linuxCommand.sh ├── software.linux.R ├── software.packages.R ├── test.R └── 诺河智苑数据下载.sh ├── statistics ├── Fundamental.statics.R ├── Logistic.function.R ├── Multicollinearity.R ├── My.stepwise.R ├── PCA.R ├── ROC.R ├── gd_logit_model.R └── logistic.R ├── survival ├── CompareModel.R ├── Cox.bootstrap.R ├── Cox.function.R ├── KM.curve.and.logrank.test.R ├── OSmaxstateCCF.R ├── Stepwise.Cox.R ├── Strata.COX.function.R ├── Test.proportional.hazards.R ├── proportionalhazardsassumption.R ├── randomForestSRC.R ├── survivalROC.R └── survival_analysis_example.r └── zhy.R /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/shijianasdf/UsualRcode/HEAD/.gitignore -------------------------------------------------------------------------------- /Annotation/hgu133plus2.db.R: -------------------------------------------------------------------------------- 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