├── README.md ├── code ├── COVID-19_metadata_repo.csv ├── COVID-19_metadata_repo_GEOidents.csv ├── additionalFunctions_repo.R ├── config.xml ├── covid_analysis_markdown.Rmd ├── exh.list.csv ├── generating_Seurat_object.Rmd ├── isg.list.csv └── sample_alignment.sh └── data ├── IPA ├── covid_555_1_B.txt ├── covid_555_1_B.ur.txt ├── covid_555_1_CD14mono.txt ├── covid_555_1_CD14mono.ur.txt ├── covid_555_1_CD16mono.txt ├── covid_555_1_CD16mono.ur.txt ├── covid_555_1_CD4T.txt ├── covid_555_1_CD4T.ur.txt ├── covid_555_1_CD8T.txt ├── covid_555_1_CD8T.ur.txt ├── covid_555_1_DC.txt ├── covid_555_1_DC.ur.txt ├── covid_555_1_NK.txt ├── covid_555_1_NK.ur.txt ├── covid_555_1_gdT.txt ├── covid_555_1_gdT.ur.txt ├── covid_555_2_B.txt ├── covid_555_2_B.ur.txt ├── covid_555_2_CD14mono.txt ├── covid_555_2_CD14mono.ur.txt ├── covid_555_2_CD16mono.txt ├── covid_555_2_CD16mono.ur.txt ├── covid_555_2_CD4T.txt ├── covid_555_2_CD4T.ur.txt ├── covid_555_2_CD8T.txt ├── covid_555_2_CD8T.ur.txt ├── covid_555_2_DC.txt ├── covid_555_2_DC.ur.txt ├── covid_555_2_NK.txt ├── covid_555_2_NK.ur.txt ├── covid_555_2_gdT.txt ├── covid_555_2_gdT.ur.txt ├── covid_556_B.txt ├── covid_556_B.ur.txt ├── covid_556_CD14mono.txt ├── covid_556_CD14mono.ur.txt ├── covid_556_CD4T.txt ├── covid_556_CD4T.ur.txt ├── covid_556_CD8T.txt ├── covid_556_CD8T.ur.txt ├── covid_556_DC.txt ├── covid_556_DC.ur.txt ├── covid_556_NK.txt ├── covid_556_NK.ur.txt ├── covid_556_gdT.txt ├── covid_556_gdT.ur.txt ├── covid_557_B.txt ├── covid_557_B.ur.txt ├── covid_557_CD14mono.txt ├── covid_557_CD14mono.ur.txt ├── covid_557_CD16mono.txt ├── covid_557_CD16mono.ur.txt ├── covid_557_CD4T.txt ├── covid_557_CD4T.ur.txt ├── covid_557_CD8T.txt ├── covid_557_CD8T.ur.txt ├── covid_557_DC.txt ├── covid_557_DC.ur.txt ├── covid_557_NK.txt ├── covid_557_NK.ur.txt ├── covid_557_gdT.txt ├── covid_557_gdT.ur.txt ├── covid_558_B.txt ├── covid_558_B.ur.txt ├── covid_558_CD14mono.txt ├── covid_558_CD14mono.ur.txt ├── covid_558_CD16mono.txt ├── covid_558_CD16mono.ur.txt ├── covid_558_CD4T.txt ├── covid_558_CD4T.ur.txt ├── covid_558_CD8T.txt ├── covid_558_CD8T.ur.txt ├── covid_558_DC.txt ├── covid_558_DC.ur.txt ├── covid_558_NK.txt ├── covid_558_NK.ur.txt ├── covid_559_B.txt ├── covid_559_B.ur.txt ├── covid_559_CD14mono.txt ├── covid_559_CD14mono.ur.txt ├── covid_559_CD16mono.txt ├── covid_559_CD16mono.ur.txt ├── covid_559_CD4T.txt ├── covid_559_CD4T.ur.txt ├── covid_559_CD8T.txt ├── covid_559_CD8T.ur.txt ├── covid_559_DC.txt ├── covid_559_DC.ur.txt ├── covid_559_NK.txt ├── covid_559_NK.ur.txt ├── covid_559_gdT.txt ├── covid_559_gdT.ur.txt ├── covid_560_B.txt ├── covid_560_B.ur.txt ├── covid_560_CD14mono.txt ├── covid_560_CD14mono.ur.txt ├── covid_560_CD16mono.txt ├── covid_560_CD16mono.ur.txt ├── covid_560_CD4T.txt ├── covid_560_CD4T.ur.txt ├── covid_560_CD8T.txt ├── covid_560_CD8T.ur.txt ├── covid_560_DC.txt ├── covid_560_DC.ur.txt ├── covid_560_NK.txt ├── covid_560_NK.ur.txt ├── covid_561_B.txt ├── covid_561_B.ur.txt ├── covid_561_CD14mono.txt ├── covid_561_CD14mono.ur.txt ├── covid_561_CD16mono.txt ├── covid_561_CD16mono.ur.txt ├── covid_561_CD4T.txt ├── covid_561_CD4T.ur.txt ├── covid_561_CD8T.txt ├── covid_561_CD8T.ur.txt ├── covid_561_DC.txt ├── covid_561_DC.ur.txt ├── covid_561_NK.txt ├── covid_561_NK.ur.txt ├── covid_561_gdT.txt ├── covid_561_gdT.ur.txt └── foo.txt └── count_matrices ├── 560_cell.counts.matrices.rds └── foo.txt /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/README.md -------------------------------------------------------------------------------- /code/COVID-19_metadata_repo.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/code/COVID-19_metadata_repo.csv -------------------------------------------------------------------------------- /code/COVID-19_metadata_repo_GEOidents.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/code/COVID-19_metadata_repo_GEOidents.csv -------------------------------------------------------------------------------- /code/additionalFunctions_repo.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/code/additionalFunctions_repo.R -------------------------------------------------------------------------------- /code/config.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/code/config.xml -------------------------------------------------------------------------------- /code/covid_analysis_markdown.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/code/covid_analysis_markdown.Rmd -------------------------------------------------------------------------------- /code/exh.list.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/code/exh.list.csv -------------------------------------------------------------------------------- /code/generating_Seurat_object.Rmd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/code/generating_Seurat_object.Rmd -------------------------------------------------------------------------------- /code/isg.list.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/code/isg.list.csv -------------------------------------------------------------------------------- /code/sample_alignment.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/code/sample_alignment.sh -------------------------------------------------------------------------------- /data/IPA/covid_555_1_B.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_1_B.txt -------------------------------------------------------------------------------- /data/IPA/covid_555_1_B.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_1_B.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_555_1_CD14mono.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_1_CD14mono.txt -------------------------------------------------------------------------------- /data/IPA/covid_555_1_CD14mono.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_1_CD14mono.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_555_1_CD16mono.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_1_CD16mono.txt -------------------------------------------------------------------------------- /data/IPA/covid_555_1_CD16mono.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_1_CD16mono.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_555_1_CD4T.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_1_CD4T.txt -------------------------------------------------------------------------------- /data/IPA/covid_555_1_CD4T.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_1_CD4T.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_555_1_CD8T.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_1_CD8T.txt -------------------------------------------------------------------------------- /data/IPA/covid_555_1_CD8T.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_1_CD8T.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_555_1_DC.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_1_DC.txt -------------------------------------------------------------------------------- /data/IPA/covid_555_1_DC.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_1_DC.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_555_1_NK.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_1_NK.txt -------------------------------------------------------------------------------- /data/IPA/covid_555_1_NK.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_1_NK.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_555_1_gdT.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_1_gdT.txt -------------------------------------------------------------------------------- /data/IPA/covid_555_1_gdT.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_1_gdT.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_555_2_B.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_2_B.txt -------------------------------------------------------------------------------- /data/IPA/covid_555_2_B.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_2_B.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_555_2_CD14mono.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_2_CD14mono.txt -------------------------------------------------------------------------------- /data/IPA/covid_555_2_CD14mono.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_2_CD14mono.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_555_2_CD16mono.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_2_CD16mono.txt -------------------------------------------------------------------------------- /data/IPA/covid_555_2_CD16mono.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_2_CD16mono.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_555_2_CD4T.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_2_CD4T.txt -------------------------------------------------------------------------------- /data/IPA/covid_555_2_CD4T.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_2_CD4T.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_555_2_CD8T.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_2_CD8T.txt -------------------------------------------------------------------------------- /data/IPA/covid_555_2_CD8T.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_2_CD8T.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_555_2_DC.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_2_DC.txt -------------------------------------------------------------------------------- /data/IPA/covid_555_2_DC.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_2_DC.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_555_2_NK.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_2_NK.txt -------------------------------------------------------------------------------- /data/IPA/covid_555_2_NK.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_2_NK.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_555_2_gdT.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_2_gdT.txt -------------------------------------------------------------------------------- /data/IPA/covid_555_2_gdT.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_555_2_gdT.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_556_B.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_556_B.txt -------------------------------------------------------------------------------- /data/IPA/covid_556_B.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_556_B.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_556_CD14mono.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_556_CD14mono.txt -------------------------------------------------------------------------------- /data/IPA/covid_556_CD14mono.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_556_CD14mono.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_556_CD4T.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_556_CD4T.txt -------------------------------------------------------------------------------- /data/IPA/covid_556_CD4T.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_556_CD4T.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_556_CD8T.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_556_CD8T.txt -------------------------------------------------------------------------------- /data/IPA/covid_556_CD8T.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_556_CD8T.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_556_DC.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_556_DC.txt -------------------------------------------------------------------------------- /data/IPA/covid_556_DC.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_556_DC.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_556_NK.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_556_NK.txt -------------------------------------------------------------------------------- /data/IPA/covid_556_NK.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_556_NK.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_556_gdT.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_556_gdT.txt -------------------------------------------------------------------------------- /data/IPA/covid_556_gdT.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_556_gdT.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_557_B.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_557_B.txt -------------------------------------------------------------------------------- /data/IPA/covid_557_B.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_557_B.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_557_CD14mono.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_557_CD14mono.txt -------------------------------------------------------------------------------- /data/IPA/covid_557_CD14mono.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_557_CD14mono.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_557_CD16mono.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_557_CD16mono.txt -------------------------------------------------------------------------------- /data/IPA/covid_557_CD16mono.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_557_CD16mono.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_557_CD4T.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_557_CD4T.txt -------------------------------------------------------------------------------- /data/IPA/covid_557_CD4T.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_557_CD4T.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_557_CD8T.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_557_CD8T.txt -------------------------------------------------------------------------------- /data/IPA/covid_557_CD8T.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_557_CD8T.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_557_DC.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_557_DC.txt -------------------------------------------------------------------------------- /data/IPA/covid_557_DC.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_557_DC.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_557_NK.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_557_NK.txt -------------------------------------------------------------------------------- /data/IPA/covid_557_NK.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_557_NK.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_557_gdT.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_557_gdT.txt -------------------------------------------------------------------------------- /data/IPA/covid_557_gdT.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_557_gdT.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_558_B.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_558_B.txt -------------------------------------------------------------------------------- /data/IPA/covid_558_B.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_558_B.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_558_CD14mono.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_558_CD14mono.txt -------------------------------------------------------------------------------- /data/IPA/covid_558_CD14mono.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_558_CD14mono.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_558_CD16mono.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_558_CD16mono.txt -------------------------------------------------------------------------------- /data/IPA/covid_558_CD16mono.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_558_CD16mono.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_558_CD4T.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_558_CD4T.txt -------------------------------------------------------------------------------- /data/IPA/covid_558_CD4T.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_558_CD4T.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_558_CD8T.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_558_CD8T.txt -------------------------------------------------------------------------------- /data/IPA/covid_558_CD8T.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_558_CD8T.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_558_DC.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_558_DC.txt -------------------------------------------------------------------------------- /data/IPA/covid_558_DC.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_558_DC.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_558_NK.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_558_NK.txt -------------------------------------------------------------------------------- /data/IPA/covid_558_NK.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_558_NK.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_559_B.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_559_B.txt -------------------------------------------------------------------------------- /data/IPA/covid_559_B.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_559_B.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_559_CD14mono.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_559_CD14mono.txt -------------------------------------------------------------------------------- /data/IPA/covid_559_CD14mono.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_559_CD14mono.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_559_CD16mono.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_559_CD16mono.txt -------------------------------------------------------------------------------- /data/IPA/covid_559_CD16mono.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_559_CD16mono.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_559_CD4T.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_559_CD4T.txt -------------------------------------------------------------------------------- /data/IPA/covid_559_CD4T.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_559_CD4T.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_559_CD8T.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_559_CD8T.txt -------------------------------------------------------------------------------- /data/IPA/covid_559_CD8T.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_559_CD8T.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_559_DC.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_559_DC.txt -------------------------------------------------------------------------------- /data/IPA/covid_559_DC.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_559_DC.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_559_NK.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_559_NK.txt -------------------------------------------------------------------------------- /data/IPA/covid_559_NK.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_559_NK.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_559_gdT.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_559_gdT.txt -------------------------------------------------------------------------------- /data/IPA/covid_559_gdT.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_559_gdT.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_560_B.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_560_B.txt -------------------------------------------------------------------------------- /data/IPA/covid_560_B.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_560_B.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_560_CD14mono.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_560_CD14mono.txt -------------------------------------------------------------------------------- /data/IPA/covid_560_CD14mono.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_560_CD14mono.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_560_CD16mono.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_560_CD16mono.txt -------------------------------------------------------------------------------- /data/IPA/covid_560_CD16mono.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_560_CD16mono.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_560_CD4T.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_560_CD4T.txt -------------------------------------------------------------------------------- /data/IPA/covid_560_CD4T.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_560_CD4T.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_560_CD8T.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_560_CD8T.txt -------------------------------------------------------------------------------- /data/IPA/covid_560_CD8T.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_560_CD8T.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_560_DC.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_560_DC.txt -------------------------------------------------------------------------------- /data/IPA/covid_560_DC.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_560_DC.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_560_NK.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_560_NK.txt -------------------------------------------------------------------------------- /data/IPA/covid_560_NK.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_560_NK.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_561_B.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_561_B.txt -------------------------------------------------------------------------------- /data/IPA/covid_561_B.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_561_B.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_561_CD14mono.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_561_CD14mono.txt -------------------------------------------------------------------------------- /data/IPA/covid_561_CD14mono.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_561_CD14mono.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_561_CD16mono.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_561_CD16mono.txt -------------------------------------------------------------------------------- /data/IPA/covid_561_CD16mono.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_561_CD16mono.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_561_CD4T.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_561_CD4T.txt -------------------------------------------------------------------------------- /data/IPA/covid_561_CD4T.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_561_CD4T.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_561_CD8T.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_561_CD8T.txt -------------------------------------------------------------------------------- /data/IPA/covid_561_CD8T.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_561_CD8T.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_561_DC.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_561_DC.txt -------------------------------------------------------------------------------- /data/IPA/covid_561_DC.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_561_DC.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_561_NK.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_561_NK.txt -------------------------------------------------------------------------------- /data/IPA/covid_561_NK.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_561_NK.ur.txt -------------------------------------------------------------------------------- /data/IPA/covid_561_gdT.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_561_gdT.txt -------------------------------------------------------------------------------- /data/IPA/covid_561_gdT.ur.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/IPA/covid_561_gdT.ur.txt -------------------------------------------------------------------------------- /data/IPA/foo.txt: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /data/count_matrices/560_cell.counts.matrices.rds: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ajwilk/2020_Wilk_COVID/HEAD/data/count_matrices/560_cell.counts.matrices.rds -------------------------------------------------------------------------------- /data/count_matrices/foo.txt: -------------------------------------------------------------------------------- 1 | 2 | --------------------------------------------------------------------------------