├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── Fig2 ├── 1.1Figure2A.rmd ├── 1.2Figure2B.rmd ├── Figure2A.csv ├── Figure2B.csv ├── Figure2_B_A.rda └── mytheme.R ├── Fig3 ├── .keep ├── Figure3A.csv └── Figure3B.csv ├── Fig4 ├── .keep ├── Figure4A.csv └── Figure4B.csv ├── Fig5 ├── .keep ├── Figure5A.csv ├── Figure5B.csv └── Figure5C.csv ├── Fig6 ├── .keep ├── Figure6A.csv ├── Figure6B.csv └── Figure6C.csv ├── LICENSE ├── LICENSE.md ├── Logo.jpg ├── NAMESPACE ├── R ├── CSS_Calculate.R └── TCSS_Calculate.R ├── README.md ├── TCellSI.Rproj ├── algorithm.jpg └── data ├── HKgenes.rda ├── exampleSample.rda ├── markers.rda └── ref_data.rda /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VyvyanYjm/TCellSI/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VyvyanYjm/TCellSI/HEAD/.gitignore -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VyvyanYjm/TCellSI/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /Fig2/1.1Figure2A.rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VyvyanYjm/TCellSI/HEAD/Fig2/1.1Figure2A.rmd -------------------------------------------------------------------------------- /Fig2/1.2Figure2B.rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VyvyanYjm/TCellSI/HEAD/Fig2/1.2Figure2B.rmd -------------------------------------------------------------------------------- /Fig2/Figure2A.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VyvyanYjm/TCellSI/HEAD/Fig2/Figure2A.csv -------------------------------------------------------------------------------- /Fig2/Figure2B.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VyvyanYjm/TCellSI/HEAD/Fig2/Figure2B.csv -------------------------------------------------------------------------------- /Fig2/Figure2_B_A.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VyvyanYjm/TCellSI/HEAD/Fig2/Figure2_B_A.rda -------------------------------------------------------------------------------- /Fig2/mytheme.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VyvyanYjm/TCellSI/HEAD/Fig2/mytheme.R -------------------------------------------------------------------------------- /Fig3/.keep: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /Fig3/Figure3A.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VyvyanYjm/TCellSI/HEAD/Fig3/Figure3A.csv -------------------------------------------------------------------------------- /Fig3/Figure3B.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VyvyanYjm/TCellSI/HEAD/Fig3/Figure3B.csv -------------------------------------------------------------------------------- /Fig4/.keep: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /Fig4/Figure4A.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VyvyanYjm/TCellSI/HEAD/Fig4/Figure4A.csv -------------------------------------------------------------------------------- /Fig4/Figure4B.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VyvyanYjm/TCellSI/HEAD/Fig4/Figure4B.csv -------------------------------------------------------------------------------- /Fig5/.keep: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /Fig5/Figure5A.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VyvyanYjm/TCellSI/HEAD/Fig5/Figure5A.csv -------------------------------------------------------------------------------- /Fig5/Figure5B.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VyvyanYjm/TCellSI/HEAD/Fig5/Figure5B.csv -------------------------------------------------------------------------------- /Fig5/Figure5C.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VyvyanYjm/TCellSI/HEAD/Fig5/Figure5C.csv -------------------------------------------------------------------------------- /Fig6/.keep: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /Fig6/Figure6A.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VyvyanYjm/TCellSI/HEAD/Fig6/Figure6A.csv -------------------------------------------------------------------------------- /Fig6/Figure6B.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VyvyanYjm/TCellSI/HEAD/Fig6/Figure6B.csv -------------------------------------------------------------------------------- /Fig6/Figure6C.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VyvyanYjm/TCellSI/HEAD/Fig6/Figure6C.csv -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | YEAR: 2024 2 | COPYRIGHT HOLDER: TCellSI authors 3 | -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VyvyanYjm/TCellSI/HEAD/LICENSE.md -------------------------------------------------------------------------------- /Logo.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VyvyanYjm/TCellSI/HEAD/Logo.jpg -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VyvyanYjm/TCellSI/HEAD/NAMESPACE -------------------------------------------------------------------------------- /R/CSS_Calculate.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VyvyanYjm/TCellSI/HEAD/R/CSS_Calculate.R -------------------------------------------------------------------------------- /R/TCSS_Calculate.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VyvyanYjm/TCellSI/HEAD/R/TCSS_Calculate.R -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VyvyanYjm/TCellSI/HEAD/README.md -------------------------------------------------------------------------------- /TCellSI.Rproj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VyvyanYjm/TCellSI/HEAD/TCellSI.Rproj -------------------------------------------------------------------------------- /algorithm.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VyvyanYjm/TCellSI/HEAD/algorithm.jpg -------------------------------------------------------------------------------- /data/HKgenes.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VyvyanYjm/TCellSI/HEAD/data/HKgenes.rda -------------------------------------------------------------------------------- /data/exampleSample.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VyvyanYjm/TCellSI/HEAD/data/exampleSample.rda -------------------------------------------------------------------------------- /data/markers.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VyvyanYjm/TCellSI/HEAD/data/markers.rda -------------------------------------------------------------------------------- /data/ref_data.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/VyvyanYjm/TCellSI/HEAD/data/ref_data.rda --------------------------------------------------------------------------------