callQoRT | Use QoRTs to get the count of subfeatures in each gene |
Combine3Re | Combine3Re |
CombineCpTftGoGeneID | CombineCpTftGoGeneID |
CompareDEfromGeneWithDEfromFeatures | CompareDEfromGeneWithDEfromFeatures |
CompareGOResults | CompareGOResults |
Draw4Cat | Draw4Cat |
Draw4GO | Draw4GO |
DrawFeature | DrawFeature |
ExtractGeneIDFromGo | ExtractGeneIDFromGo |
FDR_genewise | Title |
gene2cat | gene2cat |
gene2cat2 | gene2cat2 |
GeneBasedAnalysis | GeneBasedAnalysis |
GenerateGeneAnno | Generate gene annotations based on the Ensembl ID of genes |
GeneWisePvsExonWiseP | Compare gene based p value with exon based p value |
GetCCBetweenMostSigPadjustSJ | Title |
getDataset | codes for simulation and plot PWF simulation code from... |
GetDesign | Title |
getgo | #############################################################################... |
getgo3 | Title |
GetMgiSymbolDescription | Title |
GetMgiSymbolUsingLocalDataBase | Title |
Get_Over_under_represented_pvalue | calculate the p-value for GO terms |
GetPwfUseReformatedData | GetPwfUseReformatedData |
GetResults4GeneLevel | GetResults4GeneLevel |
GetResultsFromJunctionSeq | Get analysis results using JunctionSeq |
Gmt2GeneCat | Gmt2GeneCat |
goseq2 | goseq2 |
GotermAnalysis2GetAllGOTerms_AdjustedByNumOfJunctionWithinOneGene | This function is to subset data set based on feature |
GotermAnalysisUseFeatureDefineDE | GotermAnalysisUseFeatureDefineDE |
GotermAnalysisUseReformatedData | GotermAnalysisUseReformatedData |
GSA.read.gmt.2 | GSA.read.gmt.2 |
JS.perGeneQValue | JS.perGeneQValue |
JS.perGeneQValueExact | JS.perGeneQValueExact |
JS.perGeneQValueExact.test | Title |
LabelGeneBasedFeature | LabelGeneBasedFeature |
list_to_df | Title |
makeGeneWiseTable | This function is to generate the gene-based results |
NBsim | Generate simulated count based on NB distribution |
OuputGO | OutputGO |
OutputCatBasedPwf | OutputCatBasedPwf |
OutputFigure | Title |
OutputGeneWiseTable | Title |
OutputGOBasedDEfromFeatures | OutputGOBasedDEfromFeatures |
OutputGOBasedDEfromFeatures2 | OutputGOBasedDEfromFeatures2 |
OutputGOBasedDEfromFeatures3 | OutputGOBasedDEfromFeatures3 |
PermutattionOfRawData | Title |
plotPWF2 | Plot the probability Weighting Function |
ProcessCuffLinkResults | ProcessCuffLinkResults |
ProcessOutputFilesFrom_rMATS | ProcessOutputFilesFrom_rMATS |
readJunctionSeqCounts | Title |
ReformatData | Title |
ReformatDataUseTable | ReformatDataUseTable |
reversemapping | Title |
Select_DE_gene_basd_on_Feature | Select_DE_gene_based_on_Feature |
SelectFeature | SelectFeature |
SimulationSJ2DE | Simulate gene sets based on the number of splicing junctions |
UseLogistic2_adDE | Title |
UseLogistic2CKBias | Title |
UseOtherDataSet | Title |
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