├── 01.TCR.clone.classification.R ├── 02.TCR.specificity.R ├── 03.our.data.R ├── 03.our.data.heatmap.R ├── 04.startrac.expansion.R ├── 04.tumor.specific.T.abundance ├── 01.NSCLC1.R ├── 03.BCC.R ├── 04.SCC.R ├── 05.Breast.batch1.R ├── 06.Breast.batch2.R ├── 07.Breast.yy.R ├── 08.Renal.cell.1.R └── 09.Renal.cell.2.R ├── 05.HNSCC.data.analysis.R ├── 06.clustering ├── 02.NSCLC2.R ├── 03.BCC.R ├── 04.SCC.R ├── 05.Breast.batch1.R ├── 06.Breast.batch2.R ├── 07.Breat.yy.R ├── 08.renal.data1.R ├── 09.renal.data2.R ├── 10.renal.panT.R └── 11.all.heatmap.R ├── 07.clonal.revival.R ├── 08.CD4.tumor.specific.T.abundance ├── 01.NSCLC.R ├── 01.NSCLC.new.R ├── 02.NSCLC.Caushi.R ├── 03.BCC.R ├── 04.SCC.R ├── 05.BC.batch1.R ├── 06.BC.batch2.R ├── 07.BC.yy.R ├── 07.RC.1.R └── 08.RC.2.R ├── 09.CD4.tumor.specific.clustering ├── 01.NSCLC.R ├── 02.NSCLC.caushi.R ├── 03.BCC.R ├── 04.SCC.R └── 05.BC1.R ├── 10.CXCL13.expr └── 01.density.R ├── 11.tumor.reactive.clone.classification ├── 01.BCC.SCC.R ├── 02.SCC.R └── 03.BC.R ├── LICENSE └── README.md /01.TCR.clone.classification.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/01.TCR.clone.classification.R -------------------------------------------------------------------------------- /02.TCR.specificity.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/02.TCR.specificity.R -------------------------------------------------------------------------------- /03.our.data.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/03.our.data.R -------------------------------------------------------------------------------- /03.our.data.heatmap.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/03.our.data.heatmap.R -------------------------------------------------------------------------------- /04.startrac.expansion.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/04.startrac.expansion.R -------------------------------------------------------------------------------- /04.tumor.specific.T.abundance/01.NSCLC1.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/04.tumor.specific.T.abundance/01.NSCLC1.R -------------------------------------------------------------------------------- /04.tumor.specific.T.abundance/03.BCC.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/04.tumor.specific.T.abundance/03.BCC.R -------------------------------------------------------------------------------- /04.tumor.specific.T.abundance/04.SCC.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/04.tumor.specific.T.abundance/04.SCC.R -------------------------------------------------------------------------------- /04.tumor.specific.T.abundance/05.Breast.batch1.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/04.tumor.specific.T.abundance/05.Breast.batch1.R -------------------------------------------------------------------------------- /04.tumor.specific.T.abundance/06.Breast.batch2.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/04.tumor.specific.T.abundance/06.Breast.batch2.R -------------------------------------------------------------------------------- /04.tumor.specific.T.abundance/07.Breast.yy.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/04.tumor.specific.T.abundance/07.Breast.yy.R -------------------------------------------------------------------------------- /04.tumor.specific.T.abundance/08.Renal.cell.1.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/04.tumor.specific.T.abundance/08.Renal.cell.1.R -------------------------------------------------------------------------------- /04.tumor.specific.T.abundance/09.Renal.cell.2.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/04.tumor.specific.T.abundance/09.Renal.cell.2.R -------------------------------------------------------------------------------- /05.HNSCC.data.analysis.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/05.HNSCC.data.analysis.R -------------------------------------------------------------------------------- /06.clustering/02.NSCLC2.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/06.clustering/02.NSCLC2.R -------------------------------------------------------------------------------- /06.clustering/03.BCC.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/06.clustering/03.BCC.R -------------------------------------------------------------------------------- /06.clustering/04.SCC.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/06.clustering/04.SCC.R -------------------------------------------------------------------------------- /06.clustering/05.Breast.batch1.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/06.clustering/05.Breast.batch1.R -------------------------------------------------------------------------------- /06.clustering/06.Breast.batch2.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/06.clustering/06.Breast.batch2.R -------------------------------------------------------------------------------- /06.clustering/07.Breat.yy.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/06.clustering/07.Breat.yy.R -------------------------------------------------------------------------------- /06.clustering/08.renal.data1.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/06.clustering/08.renal.data1.R -------------------------------------------------------------------------------- /06.clustering/09.renal.data2.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/06.clustering/09.renal.data2.R -------------------------------------------------------------------------------- /06.clustering/10.renal.panT.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/06.clustering/10.renal.panT.R -------------------------------------------------------------------------------- /06.clustering/11.all.heatmap.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/06.clustering/11.all.heatmap.R -------------------------------------------------------------------------------- /07.clonal.revival.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/07.clonal.revival.R -------------------------------------------------------------------------------- /08.CD4.tumor.specific.T.abundance/01.NSCLC.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/08.CD4.tumor.specific.T.abundance/01.NSCLC.R -------------------------------------------------------------------------------- /08.CD4.tumor.specific.T.abundance/01.NSCLC.new.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/08.CD4.tumor.specific.T.abundance/01.NSCLC.new.R -------------------------------------------------------------------------------- /08.CD4.tumor.specific.T.abundance/02.NSCLC.Caushi.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/08.CD4.tumor.specific.T.abundance/02.NSCLC.Caushi.R -------------------------------------------------------------------------------- /08.CD4.tumor.specific.T.abundance/03.BCC.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/08.CD4.tumor.specific.T.abundance/03.BCC.R -------------------------------------------------------------------------------- /08.CD4.tumor.specific.T.abundance/04.SCC.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/08.CD4.tumor.specific.T.abundance/04.SCC.R -------------------------------------------------------------------------------- /08.CD4.tumor.specific.T.abundance/05.BC.batch1.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/08.CD4.tumor.specific.T.abundance/05.BC.batch1.R -------------------------------------------------------------------------------- /08.CD4.tumor.specific.T.abundance/06.BC.batch2.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/08.CD4.tumor.specific.T.abundance/06.BC.batch2.R -------------------------------------------------------------------------------- /08.CD4.tumor.specific.T.abundance/07.BC.yy.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/08.CD4.tumor.specific.T.abundance/07.BC.yy.R -------------------------------------------------------------------------------- /08.CD4.tumor.specific.T.abundance/07.RC.1.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/08.CD4.tumor.specific.T.abundance/07.RC.1.R -------------------------------------------------------------------------------- /08.CD4.tumor.specific.T.abundance/08.RC.2.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/08.CD4.tumor.specific.T.abundance/08.RC.2.R -------------------------------------------------------------------------------- /09.CD4.tumor.specific.clustering/01.NSCLC.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/09.CD4.tumor.specific.clustering/01.NSCLC.R -------------------------------------------------------------------------------- /09.CD4.tumor.specific.clustering/02.NSCLC.caushi.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/09.CD4.tumor.specific.clustering/02.NSCLC.caushi.R -------------------------------------------------------------------------------- /09.CD4.tumor.specific.clustering/03.BCC.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/09.CD4.tumor.specific.clustering/03.BCC.R -------------------------------------------------------------------------------- /09.CD4.tumor.specific.clustering/04.SCC.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/09.CD4.tumor.specific.clustering/04.SCC.R -------------------------------------------------------------------------------- /09.CD4.tumor.specific.clustering/05.BC1.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/09.CD4.tumor.specific.clustering/05.BC1.R -------------------------------------------------------------------------------- /10.CXCL13.expr/01.density.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/10.CXCL13.expr/01.density.R -------------------------------------------------------------------------------- /11.tumor.reactive.clone.classification/01.BCC.SCC.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/11.tumor.reactive.clone.classification/01.BCC.SCC.R -------------------------------------------------------------------------------- /11.tumor.reactive.clone.classification/02.SCC.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/11.tumor.reactive.clone.classification/02.SCC.R -------------------------------------------------------------------------------- /11.tumor.reactive.clone.classification/03.BC.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/11.tumor.reactive.clone.classification/03.BC.R -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PaulingLiu/metaICB/HEAD/README.md --------------------------------------------------------------------------------