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
aiminy/PathwaySJ documentation built on May 10, 2017, 9:16 p.m.