Last updated: 2025-03-06
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Knit directory: paed-airway-allTissues/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | 9c9fdaa | Gunjan Dixit | 2025-03-06 | Updated index |
| html | 3d66dc5 | Gunjan Dixit | 2025-02-28 | Updated index |
| Rmd | a179c59 | Gunjan Dixit | 2025-02-28 | Updated RUV DGE analysis |
| html | a179c59 | Gunjan Dixit | 2025-02-28 | Updated RUV DGE analysis |
| Rmd | 48174ea | Gunjan Dixit | 2025-02-07 | Added DGE analysis for Tonsils summary |
| html | 48174ea | Gunjan Dixit | 2025-02-07 | Added DGE analysis for Tonsils summary |
| Rmd | 9fe8c18 | Gunjan Dixit | 2025-02-07 | Added DGE analysis for Tonsil Atlas |
| html | 9fe8c18 | Gunjan Dixit | 2025-02-07 | Added DGE analysis for Tonsil Atlas |
| Rmd | e382550 | Gunjan Dixit | 2025-02-05 | Updated index file |
| html | 600b673 | Gunjan Dixit | 2025-02-05 | Added DGE analysis for Tonsils |
| Rmd | a9cec9b | Gunjan Dixit | 2024-12-22 | Updated indexg |
| html | a9cec9b | Gunjan Dixit | 2024-12-22 | Updated indexg |
| Rmd | b2114c7 | Gunjan Dixit | 2024-12-17 | Updated new results with more cells |
| html | b2114c7 | Gunjan Dixit | 2024-12-17 | Updated new results with more cells |
| Rmd | a2338c3 | Gunjan Dixit | 2024-10-01 | Updated index |
| html | a2338c3 | Gunjan Dixit | 2024-10-01 | Updated index |
| html | 07af966 | Gunjan Dixit | 2024-09-25 | Modified index |
| Rmd | 3b5ab22 | Gunjan Dixit | 2024-09-25 | Separated Subclustering Rmd |
| Rmd | 14f8a5e | Gunjan Dixit | 2024-05-24 | Added age analysis |
| html | 14f8a5e | Gunjan Dixit | 2024-05-24 | Added age analysis |
| Rmd | bd5ec04 | Gunjan Dixit | 2024-05-03 | Modified index |
| html | bd5ec04 | Gunjan Dixit | 2024-05-03 | Modified index |
| html | bc77c20 | Gunjan Dixit | 2024-04-26 | Build site. |
| Rmd | 9492583 | Gunjan Dixit | 2024-04-26 | Added new analysis |
| html | 9492583 | Gunjan Dixit | 2024-04-26 | Added new analysis |
| html | 8538338 | Gunjan Dixit | 2023-08-15 | Build site. |
| html | 5085c7b | Gunjan Dixit | 2023-08-11 | Build site. |
| Rmd | 2fbede2 | Gunjan Dixit | 2023-08-11 | wflow_publish("analysis/*") |
| html | 1a72faa | Gunjan Dixit | 2023-08-11 | Build site. |
| Rmd | 0bdb3ba | Gunjan Dixit | 2023-08-11 | wflow_publish("analysis/*") |
| Rmd | 50dfa03 | Gunjan Dixit | 2023-08-11 | Start workflowr project. |
This project involves the analysis of scRNA-seq data obtained from healthy tissue samples from five key locations of the respiratory system in children. The aim of this project is to develop a cell atlas of the healthy pediatric airway.
(OLD Analysis with EmptyDroplets)
Using DecontX to remove ambient RNA contamination, filtering high mitochondrial percentage outliers, using scDblFinder to identify and filter doublets and using GEM-level information to identify multiplets.
Adenoids-
G000231_Batch3
G000231_Batch8
Tonsils-
G000231_Batch2
G000231_Batch9
Nasal_brushings-
G000231_Batch1
G000231_Batch5
Bronchial_brushings-
G000231_Batch4
G000231_Batch7
BAL-
G000231_Batch6
sessionInfo()R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS 15.3.1
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: Australia/Melbourne
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_0.6.5 httr_1.4.7 cli_3.6.2 knitr_1.45
[5] rlang_1.1.3 xfun_0.42 stringi_1.8.3 processx_3.8.3
[9] promises_1.2.1 jsonlite_1.8.8 glue_1.7.0 rprojroot_2.0.4
[13] git2r_0.33.0 htmltools_0.5.7 httpuv_1.6.14 ps_1.7.6
[17] sass_0.4.8 fansi_1.0.6 rmarkdown_2.25 jquerylib_0.1.4
[21] tibble_3.2.1 evaluate_0.23 fastmap_1.1.1 yaml_2.3.8
[25] lifecycle_1.0.4 whisker_0.4.1 stringr_1.5.1 compiler_4.3.2
[29] fs_1.6.3 pkgconfig_2.0.3 Rcpp_1.0.12 rstudioapi_0.15.0
[33] later_1.3.2 digest_0.6.34 R6_2.5.1 utf8_1.2.4
[37] pillar_1.9.0 callr_3.7.5 magrittr_2.0.3 bslib_0.6.1
[41] tools_4.3.2 cachem_1.0.8 getPass_0.2-4