Last updated: 2024-12-22

Checks: 6 1

Knit directory: paed-airway-allTissues/

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Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/index.Rmd) and HTML (docs/index.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File	Version	Author	Date	Message
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.

Introduction:

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.

Overview

CellRanger Filtered Output Overview

Pre-processing: emptyDroplets

(OLD Analysis with EmptyDroplets)

Pre-processing: CellRanger

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

QC Summary

Sample-wise_QC_plots

Clustering and Marker gene Analysis:

Subclustering:

Updated Clustering and Subclustering:

Age-related changes in cell-type compositions

Propeller_Analysis: All Tissues (OLD ANALYSIS)
Adenoids
Tonsils
Nasal_brushings
Bronchial_brushings
BAL

sessionInfo()

R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS 15.2

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

Paediatric airway atlas: all Tissues

December 22, 2024