xiayh17/RNAseqStat2
A Pipeline to Process RNAseq Data

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Functions
318
Source code
44
Man pages
92
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xiayh17/RNAseqStat2: A Pipeline to Process RNAseq Data
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API

API for xiayh17/RNAseqStat2
A Pipeline to Process RNAseq Data

Global functions
%>% Man page
BaseVolcanoPlot Source code
Create_DEGContainer Man page Source code
Create_MSigDB Man page Source code
Create_dataInfo Man page Source code
Create_degResults Source code
Create_gseParam Man page Source code
Create_gseResults Source code
Create_hyperParam Man page Source code
Create_hyperResults Source code
Create_msigdbGSEAparam Man page Source code
Create_msigdbHyperParam Man page Source code
Create_msigdbParam Man page Source code
Create_treatInfo Man page Source code
Create_vsData Source code
DEGContainer Man page
DEGContainer-class Man page
DEGtopHeatmap Man page Source code
DEGvenn Man page Source code
DESeq2_qc Source code
DESeq2_res,DEGContainer-method Man page
DESeq2_res<-,DEGContainer-method Man page
DESeq2_resolve Man page Source code
FC_Identify Man page Source code
GSEA_GS Source code
GSEAbar Man page Source code
GSEAplot Man page Source code
HKG_check Man page Source code
MSigDB Man page
MSigDB-class Man page
MSigDBSummary Man page Source code
PointVolcano Man page Source code
ac_ Man page Source code
box_check Man page Source code
caseGroup Man page
caseGroup<- Man page
caseGroup<-,DEGContainer-method Man page
cleanSYMBOL Man page Source code
commonGroup Man page Source code
compareEnrichCircle Man page Source code
cor500_check Man page Source code
corall_check Man page Source code
create_volcano Source code
cutFC,DEGContainer-method Man page
cutFC<-,DEGContainer-method Man page
cutFC_Verify Man page Source code
cutFDR,DEGContainer-method Man page
cutFDR<-,DEGContainer-method Man page
cutMuch Man page Source code
dataDEG Man page Source code
dataInfo Man page
dataInfo-class Man page
dataType Man page
dataType<- Man page
dataType<-,DEGContainer-method Man page
degGroup Man page
degResolve Man page Source code
degResolveArray Man page Source code
degResults-class Man page
degSummary Man page Source code
deg_here Man page Source code
density_check Man page Source code
edgeR_res,DEGContainer-method Man page
edgeR_res<-,DEGContainer-method Man page
edgeR_resolve Man page Source code
eggnogG2T Man page Source code
enrichBar Man page Source code
enrichGO2 Man page Source code
enrichMSigDB_Core Source code
expMatrix Man page
expMatrix<- Man page
expMatrix<-,DEGContainer-method Man page
exprBox Man page Source code
exprCorHeatmap Man page Source code
exprHKGheatmap Man page Source code
exprLong Source code
exprPCA Man page Source code
exprRidges Man page Source code
exprTopHeatmap Man page Source code
filterMethod Man page
filterMethod<- Man page
filterMethod<-,DEGContainer-method Man page
geneNames Man page
geneNames<- Man page
geneNames<-,DEGContainer-method Man page
genePoint Source code
geom_volcano_point Man page Source code
geom_volcano_text Man page Source code
get_GO_data2 Source code
get_breaks Man page Source code
groupCir Man page Source code
groupInfo Man page
groupInfo<- Man page
groupInfo<-,DEGContainer-method Man page
groupLegend Source code
gseCore Source code
gseGO2 Man page Source code
gseGOparam,DEGContainer-method Man page
gseGOparam<-,DEGContainer-method Man page
gseKEGGparam,DEGContainer-method Man page
gseKEGGparam<-,DEGContainer-method Man page
gseMSigDB Man page Source code
gseRes,DEGContainer-method Man page
gseRes<-,DEGContainer-method Man page
gseResolve Man page Source code
gseSummary Man page Source code
gse_goResolve Source code
gse_keggResolve Source code
gsvaResolve Man page Source code
gsva_limma_resolve Source code
guide_enrichBar Source code
guide_enrichLegend Source code
heatCir Man page Source code
heatLegend Man page Source code
heatValues Source code
hideCir Source code
highlightGroup Man page Source code
hyperBar Man page Source code
hyperCore Source code
hyperGOparam,DEGContainer-method Man page
hyperGOparam<-,DEGContainer-method Man page
hyperKEGGparam,DEGContainer-method Man page
hyperKEGGparam<-,DEGContainer-method Man page
hyperMSigDB Man page Source code
hyperMSigDB_Resolve Man page Source code
hyperRes,DEGContainer-method Man page
hyperRes<-,DEGContainer-method Man page
hyperResolve Man page Source code
hyperSummary Man page Source code
hyperSummaryCSV Source code
hyperSummaryGOBar Source code
hyperSummaryHyperBar Source code
hyperSummaryHyperCompareCircle Source code
hyper_GS Man page Source code
hyper_goResolve Source code
hyper_keggResolve Source code
idLegend Man page Source code
idType Man page
idType<- Man page
idType<-,DEGContainer-method Man page
label,DEGContainer-method Man page
label<-,DEGContainer-method Man page
label_ns,DEGContainer-method Man page
label_ns<-,DEGContainer-method Man page
limma_res,DEGContainer-method Man page
limma_res<-,DEGContainer-method Man page
limma_resolve Man page Source code
limma_resolveArray Man page Source code
linkCir Man page Source code
matrixFiltered Man page
matrixFiltered<- Man page
matrixFiltered<-,DEGContainer-method Man page
merge_deg Source code
merge_res,DEGContainer-method Man page
merge_res<-,DEGContainer-method Man page
modelEnrich Man page Source code
msigdbData,DEGContainer-method Man page
msigdbData,MSigDB-method Man page
msigdbData<-,DEGContainer-method Man page
msigdbData<-,MSigDB-method Man page
msigdbGSEAparam,DEGContainer-method Man page
msigdbGSEAparam,MSigDB-method Man page
msigdbGSEAparam<-,DEGContainer-method Man page
msigdbGSEAparam<-,MSigDB-method Man page
msigdbGSEAresult,DEGContainer-method Man page
msigdbGSEAresult,MSigDB-method Man page
msigdbGSEAresult<-,DEGContainer-method Man page
msigdbGSEAresult<-,MSigDB-method Man page
msigdbGSVAresult,DEGContainer-method Man page
msigdbGSVAresult,MSigDB-method Man page
msigdbGSVAresult<-,DEGContainer-method Man page
msigdbGSVAresult<-,MSigDB-method Man page
msigdbGet Man page Source code
msigdbGetCore Source code
msigdbHyperParam,DEGContainer-method Man page
msigdbHyperParam,MSigDB-method Man page
msigdbHyperParam<-,DEGContainer-method Man page
msigdbHyperParam<-,MSigDB-method Man page
msigdbHyperResult,DEGContainer-method Man page
msigdbHyperResult,MSigDB-method Man page
msigdbHyperResult<-,DEGContainer-method Man page
msigdbHyperResult<-,MSigDB-method Man page
msigdbParam,DEGContainer-method Man page
msigdbParam,MSigDB-method Man page
msigdbParam<-,DEGContainer-method Man page
msigdbParam<-,MSigDB-method Man page
msigdbTreat,DEGContainer-method Man page
msigdbTreat,MSigDB-method Man page
msigdbTreat<-,DEGContainer-method Man page
msigdbTreat<-,MSigDB-method Man page
newDEGContainer Man page Source code
paletteCir Man page Source code
paramParse Source code
pca_check Man page Source code
plot_boxplot_base Source code
presetSpecies Source code
pvalue_Identify Man page Source code
rectCir Man page Source code
rectCirDiscrete Man page Source code
runALL Man page Source code
runCheck Man page Source code
runDEG Man page
runGSEA Man page
runHyper Man page
runMSigDB Man page
sampleNames Man page
sampleNames<- Man page
sampleNames<-,DEGContainer-method Man page
shotSpecies Source code
sigAlpha,DEGContainer-method Man page
sigAlpha<-,DEGContainer-method Man page
sigCol,DEGContainer-method Man page
sigCol<-,DEGContainer-method Man page
sigShape,DEGContainer-method Man page
sigShape<-,DEGContainer-method Man page
sigSize,DEGContainer-method Man page
sigSize<-,DEGContainer-method Man page
species Man page
species<- Man page
species<-,DEGContainer-method Man page
textBarData Man page Source code
theme_enrichBar Source code
theme_normal Source code
theme_volcano Man page Source code
theme_wide Source code
toSYMBOL Man page Source code
top1000_check Man page Source code
topGene Man page Source code
treatInfo,DEGContainer-method Man page
treatInfo-class Man page
treatInfo<-,DEGContainer-method Man page
upDate_cutFC_NULL Source code
volcano_nudge_x_down Man page Source code
volcano_nudge_x_up Man page Source code
vsData,DEGContainer-method Man page
vsData<-,DEGContainer-method Man page
xiayh17/RNAseqStat2 documentation built on May 27, 2023, 12:13 p.m.

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