├── .Rbuildignore ├── .Rhistory ├── DESCRIPTION ├── NAMESPACE ├── R ├── CreateObject_fromSeurat.R ├── GSEA.R ├── LR2TF.R ├── ViewInterCircos.R ├── counts2rpm.R ├── data2Bubble.R ├── data2ConnectProfile.R ├── getCorrelatedGene.R ├── getDistanceKEGG.R ├── getPheatmap.R ├── getSignificantPathway.R ├── myGSEAplot.R ├── plotBubble.R ├── sankey.R ├── sankey3D.R ├── shellyFunction.R ├── step0_createObject.R ├── step1_TransConnectProfile.R └── tfRidgeplot.R ├── README.md ├── cellcall.Rproj ├── inst └── extdata │ ├── KEGG_SYMBOL_ID.txt │ ├── example_Data.Rdata │ ├── homo │ ├── exon_sum.Rdata │ └── transcriptmaxLength.Rdata │ ├── mmus │ ├── exon_sum.Rdata │ └── transcriptmaxLength.Rdata │ ├── new_ligand_receptor_TFs.txt │ ├── new_ligand_receptor_TFs_extended.txt │ ├── new_ligand_receptor_TFs_homology.txt │ ├── new_ligand_receptor_TFs_homology_extended.txt │ ├── tf_target.txt │ └── tf_target_homology.txt └── man ├── CellInter-class.Rd ├── ConnectProfile.Rd ├── CreateNichConObject.Rd ├── LR2TF.Rd ├── LRT.Dimplot.Rd ├── TransCommuProfile.Rd ├── ViewInterCircos.Rd ├── counts2normalized_10X.Rd ├── counts2normalized_smartseq2.Rd ├── getCorrelatedGene.Rd ├── getDistanceKEGG.Rd ├── getForBubble.Rd ├── getGSEA.Rd ├── getGSEAplot.Rd ├── getHyperPathway.Rd ├── mylog2foldChange.diy.Rd ├── plotBubble.Rd ├── ridgeplot.DIY.Rd ├── sankey_graph.Rd ├── trans2tripleScore.Rd └── viewPheatmap.Rd /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShellyCoder/cellcall/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.Rhistory: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ShellyCoder/cellcall/HEAD/.Rhistory -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- 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