Files in aiminy/PathwaySJ
A R package for GO term enrichment analysis with the flexible bias factor adjustment
DESCRIPTION
Figure/20160213_094438.png
Figure/BiasFromGeneStructure.png
Figure/gene_feature_DE.tiff
Figure/pwFeatureFeature.pdf
Figure/pwFeatureFeature.tiff
Figure/pwfFeatureGL.pdf
Figure/pwfFeatureGL.tiff
Figure/pwfGeneFeature.pdf
Figure/pwfGeneFeature.tiff
Figure/pwfGeneGL.pdf
Figure/pwfGeneGL.tiff
Figure/sjvsGL.png
Figure/sjvsexons.png
Figure/working_flow.png
GOSJ.Rmd
GOSJ.Rproj
GOSJ_PJ.Rmd
GOSJ_ver_1.0.Rmd
NAMESPACE
R/03.AllClasses.R
R/AdaptedCodes_juncbias.R
R/Combine3Re.R
R/CombineCpTftGoGeneID.R
R/CompareDEfromGeneWithDEfromFeatures.R
R/CompareGOResults.R
R/DE_based_on_gene_count.R
R/Draw4Cat.R
R/Draw4GO.R
R/DrawFeature.R
R/ExtractGeneIDFromGo.R
R/FDR_genewise.R
R/GSA.read.gmt.2.R
R/GeneBasedAnalysis.R
R/GeneWisePvsExonWiseP.R
R/GenerateGeneAnno.R
R/GetCCBetweenMostSigPadjustSJ.R
R/GetDesign.R
R/GetMgiSymbolDescription.R
R/GetMgiSymbolUsingLocalDataBase.R
R/GetPwfUseReformatedData.R
R/GetResults4GeneLevel.R
R/Get_Over_under_represented_pvalue.R
R/Gmt2GeneCat.R
R/GotermAnalysis2GetAllGOTerms_AdjustedByNumOfJunctionWithinOneGene.R
R/GotermAnalysisUseFeatureDefineDE.R
R/GotermAnalysisUseReformatedData.R
R/IntsallOtherPackage.R
R/JS.perGeneQValue.R
R/JS.perGeneQValueExact.R
R/JS.perGeneQValueExact_test.R
R/LabelGeneBasedFeature.R
R/MakeGeneWiseTable_JunctionSeq.R
R/NBsim.R
R/OutputCatBasedPwf.R
R/OutputFigure.R
R/OutputGO.R
R/OutputGOBasedDEfromFeature3.R
R/OutputGOBasedDEfromFeatures.R
R/OutputGOBasedDEfromFeatures2.R
R/OutputGeneWiseTable.R
R/OutputGo.R
R/PermutationOfRawData.R
R/PlotPWF_modified.R
R/ProcessCufflink.R
R/ProcessOutputFilesFrom_rMATS.R
R/ReformatData.R
R/ReformatDataUseTable.R
R/Run_get_results_from_JunctionSeq.R
R/SelectFeature.R
R/Select_DE_gene_based_on_Feature.R
R/SimulationSJ2DE.R
R/UseLogistic2CKBias.R
R/UseLogistic2_adDE.R
R/UseOtherDataSet.R
R/ZZZ.R
R/callQoRT.R
R/gene2cat.R
R/gene2cat2.R
R/getgo2.R
R/getgo3.R
R/goseq2.R
R/list_to_df.R
R/plotPWF2.R
R/readJunctionSeqCounts.R
R/reversemapping.R
README.md
Splicing-network.bib
data/6_Samples_Count_data.csv
data/example.sj.6.samples.csv
data/gene.model.RData
data/gene.model.hg38.RData
data/genes.RData
data/genes_table_02052016.csv
man/Combine3Re.Rd
man/CombineCpTftGoGeneID.Rd
man/CompareDEfromGeneWithDEfromFeatures.Rd
man/CompareGOResults.Rd
man/Draw4Cat.Rd
man/Draw4GO.Rd
man/DrawFeature.Rd
man/ExtractGeneIDFromGo.Rd
man/FDR_genewise.Rd
man/GSA.read.gmt.2.Rd
man/GeneBasedAnalysis.Rd
man/GeneWisePvsExonWiseP.Rd
man/GenerateGeneAnno.Rd
man/GetCCBetweenMostSigPadjustSJ.Rd
man/GetDesign.Rd
man/GetMgiSymbolDescription.Rd
man/GetMgiSymbolUsingLocalDataBase.Rd
man/GetPwfUseReformatedData.Rd
man/GetResults4GeneLevel.Rd
man/GetResultsFromJunctionSeq.Rd
man/Get_Over_under_represented_pvalue.Rd
man/Gmt2GeneCat.Rd
man/GotermAnalysis2GetAllGOTerms_AdjustedByNumOfJunctionWithinOneGene.Rd
man/GotermAnalysisUseFeatureDefineDE.Rd
man/GotermAnalysisUseReformatedData.Rd
man/JS.perGeneQValue.Rd
man/JS.perGeneQValueExact.Rd
man/JS.perGeneQValueExact.test.Rd
man/LabelGeneBasedFeature.Rd
man/NBsim.Rd
man/OuputGO.Rd
man/OutputCatBasedPwf.Rd
man/OutputFigure.Rd
man/OutputGOBasedDEfromFeatures.Rd
man/OutputGOBasedDEfromFeatures2.Rd
man/OutputGOBasedDEfromFeatures3.Rd
man/OutputGeneWiseTable.Rd
man/PermutattionOfRawData.Rd
man/ProcessCuffLinkResults.Rd
man/ProcessOutputFilesFrom_rMATS.Rd
man/ReformatData.Rd
man/ReformatDataUseTable.Rd
man/SelectFeature.Rd
man/Select_DE_gene_basd_on_Feature.Rd
man/SimulationSJ2DE.Rd
man/UseLogistic2CKBias.Rd
man/UseLogistic2_adDE.Rd
man/UseOtherDataSet.Rd
man/callQoRT.Rd
man/gene2cat.Rd
man/gene2cat2.Rd
man/getDataset.Rd
man/getgo.Rd
man/getgo3.Rd
man/goseq2.Rd
man/list_to_df.Rd
man/makeGeneWiseTable.Rd
man/plotPWF2.Rd
man/readJunctionSeqCounts.Rd
man/reversemapping.Rd
