├── BriseisEncoder ├── Atchley_factors.csv ├── BriseisEncoder.py ├── OutputAccTest.py ├── Sup. Fig. 1.pdf ├── TrainedEncoder.h5 └── exampleCMD.sh ├── README.md ├── Tessa ├── MCMC_control.R ├── initialization.R ├── post_analysis.R ├── real_data.R ├── simulation.R ├── update.R └── utility.R ├── Tessa_main.py ├── Tessa_released_data ├── Kidney-bulkRNA.csv └── Kidney-scRNA.csv ├── example_data ├── embedding_example_fig.png ├── example_TCRembedding.csv ├── example_TCRmeta.csv ├── example_exp.csv ├── exp_example_fig.png ├── fixed_b.csv ├── meta_example_fig.png ├── result_meta_example.csv ├── result_meta_example_fig.png └── result_tessa_final_example.RData └── tessa_dependencies.txt /BriseisEncoder/Atchley_factors.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jcao89757/TESSA/HEAD/BriseisEncoder/Atchley_factors.csv -------------------------------------------------------------------------------- /BriseisEncoder/BriseisEncoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jcao89757/TESSA/HEAD/BriseisEncoder/BriseisEncoder.py -------------------------------------------------------------------------------- /BriseisEncoder/OutputAccTest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jcao89757/TESSA/HEAD/BriseisEncoder/OutputAccTest.py -------------------------------------------------------------------------------- /BriseisEncoder/Sup. Fig. 1.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jcao89757/TESSA/HEAD/BriseisEncoder/Sup. Fig. 1.pdf -------------------------------------------------------------------------------- /BriseisEncoder/TrainedEncoder.h5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jcao89757/TESSA/HEAD/BriseisEncoder/TrainedEncoder.h5 -------------------------------------------------------------------------------- /BriseisEncoder/exampleCMD.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jcao89757/TESSA/HEAD/BriseisEncoder/exampleCMD.sh -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jcao89757/TESSA/HEAD/README.md -------------------------------------------------------------------------------- /Tessa/MCMC_control.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jcao89757/TESSA/HEAD/Tessa/MCMC_control.R -------------------------------------------------------------------------------- /Tessa/initialization.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jcao89757/TESSA/HEAD/Tessa/initialization.R -------------------------------------------------------------------------------- /Tessa/post_analysis.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jcao89757/TESSA/HEAD/Tessa/post_analysis.R -------------------------------------------------------------------------------- /Tessa/real_data.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jcao89757/TESSA/HEAD/Tessa/real_data.R -------------------------------------------------------------------------------- /Tessa/simulation.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jcao89757/TESSA/HEAD/Tessa/simulation.R -------------------------------------------------------------------------------- /Tessa/update.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jcao89757/TESSA/HEAD/Tessa/update.R -------------------------------------------------------------------------------- /Tessa/utility.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jcao89757/TESSA/HEAD/Tessa/utility.R -------------------------------------------------------------------------------- /Tessa_main.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jcao89757/TESSA/HEAD/Tessa_main.py -------------------------------------------------------------------------------- /Tessa_released_data/Kidney-bulkRNA.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jcao89757/TESSA/HEAD/Tessa_released_data/Kidney-bulkRNA.csv -------------------------------------------------------------------------------- /Tessa_released_data/Kidney-scRNA.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jcao89757/TESSA/HEAD/Tessa_released_data/Kidney-scRNA.csv -------------------------------------------------------------------------------- /example_data/embedding_example_fig.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jcao89757/TESSA/HEAD/example_data/embedding_example_fig.png -------------------------------------------------------------------------------- /example_data/example_TCRembedding.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jcao89757/TESSA/HEAD/example_data/example_TCRembedding.csv -------------------------------------------------------------------------------- /example_data/example_TCRmeta.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jcao89757/TESSA/HEAD/example_data/example_TCRmeta.csv -------------------------------------------------------------------------------- /example_data/example_exp.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jcao89757/TESSA/HEAD/example_data/example_exp.csv -------------------------------------------------------------------------------- /example_data/exp_example_fig.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jcao89757/TESSA/HEAD/example_data/exp_example_fig.png -------------------------------------------------------------------------------- /example_data/fixed_b.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jcao89757/TESSA/HEAD/example_data/fixed_b.csv -------------------------------------------------------------------------------- /example_data/meta_example_fig.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jcao89757/TESSA/HEAD/example_data/meta_example_fig.png -------------------------------------------------------------------------------- /example_data/result_meta_example.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jcao89757/TESSA/HEAD/example_data/result_meta_example.csv -------------------------------------------------------------------------------- /example_data/result_meta_example_fig.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jcao89757/TESSA/HEAD/example_data/result_meta_example_fig.png -------------------------------------------------------------------------------- /example_data/result_tessa_final_example.RData: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jcao89757/TESSA/HEAD/example_data/result_tessa_final_example.RData -------------------------------------------------------------------------------- /tessa_dependencies.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jcao89757/TESSA/HEAD/tessa_dependencies.txt --------------------------------------------------------------------------------