• Abstract
  • Authors
  • Analysis Overview
    • Quality control
  • Licenses
  • Citations
  • Version Information

Last updated: 2024-04-27

Checks: 7 0

Knit directory: paed-inflammation-CITEseq/

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Follow the links below to view the different parts of the analysis.

Abstract

Authors

Analysis Overview

Quality control

  1. Empty droplet removal and demultiplexing

    1. Batch 0
    2. Batch 1
    3. Batch 2
    4. Batch 3
    5. Batch 4
    6. Batch 5
    7. Batch 6

  2. Quality control

  3. Identify doublets

  4. Filter doublets

  5. Remove ambient contamination

  6. Annotate using Human Lung Cell Atlas v2.0

  7. Integrate and cluster T-cells

  8. Integrate and cluster other cells

  9. Integrate and cluster macrophage cells

To ensure reproducibility, I had to install these versions of the following packages specifically: Seurat_4.4.0, SeuratObject_4.1.4, SeuratData_0.2.2 (very specifically this commit “”, Azimuth_0.4.6.

As per this issue, https://github.com/satijalab/seurat-object/issues/165, if there is an error running sctransform, remove all relevant packages (and purge if using renv) and then install using the following method exactly, to build from source.

if (!requireNamespace(“remotes”, quietly = TRUE)) { install.packages(“remotes”) } options(repos = c(“https://satijalab.r-universe.dev”, getOption(“repos”))) remotes::install_version(“SeuratObject”, “4.1.4”) remotes::install_version(“Seurat”, “4.4.0”, upgrade = FALSE) # remotes will try to upgrade SeuratObject to v5, we need to tell it no

Licenses

The code in this analysis is covered by the MIT license and the written content on this website is covered by a Creative Commons CC-BY license.

Citations

Version Information

R version: R version 4.3.3 (2024-02-29)

Bioconductor version: 3.18


sessionInfo()
R version 4.3.3 (2024-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.1 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
 [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8   
 [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       

time zone: Etc/UTC
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
[1] workflowr_1.7.1

loaded via a namespace (and not attached):
 [1] jsonlite_1.8.8      compiler_4.3.3      BiocManager_1.30.22
 [4] renv_1.0.3          promises_1.2.1      Rcpp_1.0.12        
 [7] stringr_1.5.1       git2r_0.33.0        callr_3.7.3        
[10] later_1.3.2         jquerylib_0.1.4     yaml_2.3.8         
[13] fastmap_1.1.1       R6_2.5.1            knitr_1.45         
[16] tibble_3.2.1        rprojroot_2.0.4     bslib_0.6.1        
[19] pillar_1.9.0        rlang_1.1.3         utf8_1.2.4         
[22] cachem_1.0.8        stringi_1.8.3       httpuv_1.6.14      
[25] xfun_0.42           getPass_0.2-4       fs_1.6.3           
[28] sass_0.4.8          cli_3.6.2           magrittr_2.0.3     
[31] ps_1.7.6            digest_0.6.34       processx_3.8.3     
[34] rstudioapi_0.15.0   lifecycle_1.0.4     vctrs_0.6.5        
[37] evaluate_0.23       glue_1.7.0          whisker_0.4.1      
[40] fansi_1.0.6         rmarkdown_2.25      httr_1.4.7         
[43] tools_4.3.3         pkgconfig_2.0.3     htmltools_0.5.7