Man pages for xiayh17/RNAseqStat2
A Pipeline to Process RNAseq Data
| ac_ | add group info for heatmap |
| box_check | Boxplot of expression matrix |
| cleanSYMBOL | Convert a data to SYMBOL named |
| commonGroup | Title |
| compareEnrichCircle | Plot circos of common ID |
| cor500_check | Correlation of all samples and top 500 genes |
| corall_check | Correlation of all samples and all genes |
| Create_dataInfo | create 'dataInfo' |
| Create_DEGContainer | Create 'DEGContainer' |
| Create_gseParam | Create param for gse analysis |
| Create_hyperParam | Create param for hyper analysis |
| Create_MSigDB | Create 'MSigDB' |
| Create_msigdbGSEAparam | Create 'msigdbGSEAparam' |
| Create_msigdbHyperParam | Create 'msigdbHyperParam' |
| Create_msigdbParam | Create 'MSigDB' |
| Create_treatInfo | Function for treatInfo |
| cutFC_Verify | Verify the rationality of the FC threshold |
| cutMuch | Group result of DEG analysis results |
| dataDEG | get deg data of DEGContainer |
| dataInfo | Class 'dataInfo' |
| DEGContainer | Class 'DEGContainer' |
| degGroup | Group degResults |
| deg_here | Test for exists of DEG results |
| degResolve | run DEG minimal |
| degResolveArray | run DEG minimal |
| degResults | a S4 class contains degResults from deg analysis |
| degSummary | Summary results of DEG analysis |
| DEGtopHeatmap | Heatmap for DEG data frame |
| DEGvenn | Plot venn for a set of gene |
| density_check | Density of expression matrix |
| DESeq2_resolve | Basic produce of DESeq2 |
| edgeR_resolve | Basic produce of edgeR |
| eggnogG2T | Convert EGGnog to GENE2TERM |
| enrichBar | enrich bar plot |
| enrichGO2 | GO Enrichment Analysis of a gene set. |
| exprBox | Boxplot of all samples |
| exprCorHeatmap | Correlation Heatmap between samples |
| exprHKGheatmap | Human housekeeping genes Heatmap |
| exprPCA | PCA plot for Grouped Samples |
| exprRidges | Ridges plot of all samples |
| exprTopHeatmap | Expression Heatmap |
| FC_Identify | Identify the column where the FC is located |
| geom_volcano_point | A preset geom of 'geom_point' |
| geom_volcano_text | A preset geom of 'geom_text_repel' |
| get_breaks | Values break parameters 'scale_colour_identity' |
| groupCir | Group circlize matrix |
| GSEAbar | gseKEGG bar plot |
| GSEAplot | plot gseKEGG plot |
| gseGO2 | gseGO2 |
| gseMSigDB | GSE analysis of MSigDB data sets |
| gseResolve | GSEA analysis |
| gseSummary | Summary GSE results |
| gsvaResolve | GSVA analysis |
| heatCir | heatmap values for annotation circlize |
| heatLegend | Legend for heatmap |
| highlightGroup | Group highlight |
| HKG_check | Human housekeeping genes expression |
| hyperBar | hyper barplot |
| hyper_GS | Get a significant difference gene list |
| hyperMSigDB | Hyper analysis of DEGContainer |
| hyperMSigDB_Resolve | Hyper analysis for MSigDB |
| hyperResolve | Resolve Hyper |
| hyperSummary | Summary Hyper results |
| idLegend | Legend for ID |
| limma_resolve | Basic produce of limma |
| limma_resolveArray | Basic produce of limma |
| linkCir | Create matrix for circlize chordDiagram |
| modelEnrich | Get circlize data from obj after hyper analysis |
| MSigDB | Class 'MSigDB' |
| msigdbGet | Download MSigDB data for DEGContainer |
| MSigDBSummary | Summary MSigDB modules results |
| newDEGContainer | Initialize an object of class 'DEGContainer' |
| paletteCir | Create a palette of ID across different group |
| pca_check | PCA QC check |
| pipe | Pipe operator |
| PointVolcano | Showing gene labels and highlighting gene points in a volcano... |
| pvalue_Identify | Identify the column where the pvalue is located |
| rectCir | Plot rect in continuous value |
| rectCirDiscrete | plot rect in discrete value |
| runALL | run all workflow |
| runCheck | Check you data by PCA and Heatmaps |
| runDEG | run DEG analysis |
| runGSEA | runGSEA Module |
| runHyper | runHyper |
| runMSigDB | run MSigDB module |
| textBarData | shape data of enrichResult |
| theme_volcano | theme_volcano |
| top1000_check | Heatmap of all samples and Top1000 genes |
| topGene | Choose top genes from DEG data frame of limma DESeq2 edgeR |
| toSYMBOL | Convert a ENSEMBL named data to SYMBOL named |
| volcano_nudge_x_down | nudge gene labels in x direction in down side |
| volcano_nudge_x_up | nudge gene labels in x direction in up side |
