Last updated: 2024-12-24
Checks: 5 1
Knit directory: proj_distal/analysis/
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This website displays the analysis code and results reported in the article by Cardon et al.: “Single cell profiling of circulating autoreactive CD4 T cells from patients with autoimmune liver diseases suggests tissue imprinting.” In that study, the authors performed different scRNA-seq + scTCR-seq analyses on antigen-specific circulating CD4 T cell subsets in autoimmune liver disease (AILD) to identify the transcriptional profile of pathogenic T helper cells and identify liver tissue-imprinted signatures.
Follow the links below to access the different stages of analysis or refer to the Getting started page for more details about the dataset and how to reproduce the analysis from [the processed data][zenodo].
This website and the analysis code can be cited as:
Cardon et al.: “Single cell profiling of circulating autoreactive CD4 T cells from patients with autoimmune liver diseases suggests tissue imprinting” DOI: [10.1101/2024.03.26.586770][bioRxiv]
devtools::session_info()
sessionInfo()R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS
Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_1.0.8 rstudioapi_0.13 knitr_1.37 magrittr_2.0.2
[5] workflowr_1.7.1 here_1.0.1 R6_2.5.1 rlang_1.1.1
[9] fastmap_1.1.0 fansi_1.0.2 stringr_1.4.0 tools_4.1.2
[13] xfun_0.30 utf8_1.2.2 cli_3.6.1 git2r_0.33.0
[17] jquerylib_0.1.4 htmltools_0.5.2 ellipsis_0.3.2 rprojroot_2.0.2
[21] yaml_2.3.5 digest_0.6.29 tibble_3.1.8 lifecycle_1.0.3
[25] crayon_1.5.0 later_1.3.0 sass_0.4.0 vctrs_0.6.4
[29] promises_1.2.0.1 fs_1.5.2 glue_1.6.2 evaluate_0.15
[33] rmarkdown_2.11 stringi_1.7.6 bslib_0.3.1 compiler_4.1.2
[37] pillar_1.7.0 jsonlite_1.8.0 httpuv_1.6.5 pkgconfig_2.0.3