#This project contains the codes for diverse down-stream analyses of A-to-I RNA editing in human pan-cancers from TCGA
#1. doanload links related to the project. Tool: LiftOver Download.sh Download_Gene_expression_Data.R ExtractUTR.R
#2. RNA editing detection. RNAdetection.sh
#3. RNA editing annotations in genes, regions, and repeats. RNAeditingGeneralAnnotation.sh
#4. RNA editing frequencies analysis. SpecificRNAeditingAnnotation.sh DifferentialEditing.R StageCorrelation.R SurvivalAnalysis.R Roman2Num.R Heatmap.R generate_ucsc_bed.sh
#5. Correlations between RNA editng and gene expression (ADAR enzymes). ExpressionRNAeditingAnnotation.sh ExpressionCorrelation.R Heatmap.R ADARCorrelation.R DifferentialExpression.R StageExpressionCorrelation.R Roman2Num.R SurvivalExpressionAnalysis.R
#6. annotation of RNA editing in protein-coding regions. RNAeditingProteinAnnotation.sh
#7. Correlation of RNA editing and Splicing. Tools: MaxEntScan RNAeditingSplicing.sh SplicingCorrelation.R DifferentialSplicing.R Heatmap.R
#8. Annotation of RNA editing effects on miRNA binding and regulation. Tools: TargetScan and miRanda RNAeditingMiRNA.sh CompeteComputeTwo.R Network.R
#9. Annotation of RNA editing effects on RNA structure. Tool: RNAfold RNAeditingStructureAnnotation.sh
#10. Statistics including all criteria for each part. Statistic.sh BarPlot.R Boxplot.R BubblePlot.R Enrichment.R Histogram.R VennPlot.R Violin.R VolcanoPlot.R
#11. Analyses results. https://ccsm.uth.edu/CAeditome/index.html
#12. citation. Wu S, Fan Z, Kim P, Huang L, and Zhou X, CAeditome: functional annotation of A-to-I RNA editing in patients with cancer.