Last updated: 2024-11-06
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Knit directory: CCL19_FRCs_lung_cancer/
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| Rmd | 56cd3c3 | Pchryssa | 2024-08-21 | NSCLC stroma CCCL19 FRC |
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Figure 1 and Supplementary Figure 2
Characterize stroma cells (CD90⁺ and CD90− fibroblasts and endothelial cells (EC) and primarily focus on CCL19⁺ fibroblasts : NSCLC_stroma_CCCL19_FRC.html
Compare NSCLC CCL19 FRCs with Tonsilar FRCs : NSCLC_vs_Tonsils.html
Compare NSCLC CCL19 FRCs with NSCLC and BRCA CAFs : NSCLC_vs_BRCA_CAFs.html
Figure 3 and Supplementary Figure 3
Characterize and visualize Tumor infiltrating lymphocytes (TILs), with a focus on CD8⁺ T cell subsets : NSCLC_TILS.html
Combine NSCLS CCL19⁺ FRCs and NSCLS TILs (special focus on CD8⁺ T cells ) and perform interactome analysis to determine significant signaling L-R pairs and genes involved : merge_NSCLC_FRC_TIL.html
Figure 4 and Supplementary Figure 4
Figure 5
Figure 6 and Supplementary Figure 5
Figure 7, Supplementary Figure 5 and Supplementary Figure 6
Characterize GP33/34⁺ CD8⁺ T cells sorted from LLC-gp33 bearing DTR⁺ and DTR\(^−\) lungs on day 23, after mCOV-Flt3l-gp33 immunization : Tetra_CD8_T_cells.html
Characterize total CD8 T cells in DTR lungs and perform interactome analysis between TLS TRC, Sulf1⁺ TRC and Tetramer⁺ CD8⁺ T cells : Total_CD8_DTR_Tetra.html
Comparison of naive CCL19-EYFP cells vs mCOV-FIt31-g33 CCL19-EYFP cells : mcov_R.html
sessionInfo()R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.6.9
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/Zurich
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] workflowr_1.7.1
loaded via a namespace (and not attached):
[1] vctrs_0.6.3 httr_1.4.6 cli_3.6.1 knitr_1.43
[5] rlang_1.1.1 xfun_0.39 stringi_1.7.12 processx_3.8.2
[9] promises_1.2.0.1 jsonlite_1.8.7 glue_1.6.2 rprojroot_2.0.3
[13] git2r_0.33.0 htmltools_0.5.5 httpuv_1.6.11 ps_1.7.5
[17] sass_0.4.7 fansi_1.0.4 rmarkdown_2.23 jquerylib_0.1.4
[21] tibble_3.2.1 evaluate_0.21 fastmap_1.1.1 yaml_2.3.7
[25] lifecycle_1.0.3 whisker_0.4.1 stringr_1.5.0 compiler_4.3.1
[29] fs_1.6.3 pkgconfig_2.0.3 Rcpp_1.0.11 rstudioapi_0.15.0
[33] later_1.3.1 digest_0.6.33 R6_2.5.1 utf8_1.2.3
[37] pillar_1.9.0 callr_3.7.3 magrittr_2.0.3 bslib_0.5.0
[41] tools_4.3.1 cachem_1.0.8 getPass_0.2-4