Last updated: 2024-02-19

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Knit directory: protocol_synovial/

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Unstaged changes:
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    Modified:   analysis/index.Rmd
    Modified:   analysis/scRNAseq_protocol_04-2_Annotation_marker_genes.Rmd
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File Version Author Date Message
html d6b1b5f Reto Gerber 2023-05-30 update to new version
html 91496f3 Reto Gerber 2022-05-28 update figures to final paper version
html 8644bb4 Reto Gerber 2022-05-20 update figures
Rmd 70d3496 Reto Gerber 2022-04-25 rerun with lower resolution
html 70d3496 Reto Gerber 2022-04-25 rerun with lower resolution
html 1d37a4f Reto Gerber 2022-03-29 Update analysis
html 36e8b3f Reto Gerber 2022-03-10 rerun 03 for batch quantification
html 24ea719 Reto Gerber 2022-03-07 start with v3
html 2681831 Reto Gerber 2021-12-06 Update Figures, add extra clusters
html d356ec0 Reto Gerber 2021-08-27 Include summary figures for all data and subset
Rmd 9303595 Reto Gerber 2021-08-23 Add missing file to index
html 9303595 Reto Gerber 2021-08-23 Add missing file to index
Rmd 00c7f79 Reto Gerber 2021-08-23 Update analysis to include more samples
html 00c7f79 Reto Gerber 2021-08-23 Update analysis to include more samples
html 5d722d6 Reto Gerber 2021-07-26 Rerun complete analysis
Rmd 841cd31 Reto Gerber 2021-07-06 Rerun complete analysis
html 841cd31 Reto Gerber 2021-07-06 Rerun complete analysis
Rmd 9e71f9f Reto Gerber 2021-06-21 update about and index, link to LICENCE
html 9e71f9f Reto Gerber 2021-06-21 update about and index, link to LICENCE
html d2f2dc6 Reto Gerber 2021-06-21 update index
html 6b00da0 Reto Gerber 2021-06-17 Update preprocessing script
Rmd 70dbd9e Reto Gerber 2021-06-15 update index
html 70dbd9e Reto Gerber 2021-06-15 update index
Rmd e4a1113 Reto Gerber 2021-06-11 update analysis
html e4a1113 Reto Gerber 2021-06-11 update analysis
Rmd 2cdcf57 Reto Gerber 2021-05-31 Start workflowr project.

This repo contains the scripts for the paper “A comprehensive single-cell atlas of freshly-dissociated human synovium in inflammatory arthritis with optimized dissociation protocol for prospective synovial tissue collection”.

The following is a list of the available scripts, to be run in the given order.

Analysis

  1. Preprocessing (Last modified: 2022-10-28 )
  2. HVG selection, Dimensionality reduction (Last modified: 2022-10-28 )
  3. Batch removal, Clustering (Last modified: 2022-10-28 )
  4. Annotation + subcelltypes
  5. Differential state analysis (Last modified: 2023-10-27 )
  6. Figures

A note on how to rerun the analysis is given in the About page.


sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04 LTS

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C         
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

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

other attached packages:
[1] magrittr_2.0.1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6        whisker_0.4       knitr_1.31        workflowr_1.7.0  
 [5] here_1.0.1        R6_2.5.0          rlang_0.4.10      stringr_1.4.0    
 [9] tools_4.0.3       xfun_0.21         git2r_0.30.1      htmltools_0.5.1.1
[13] ellipsis_0.3.1    yaml_2.2.1        digest_0.6.27     rprojroot_2.0.2  
[17] tibble_3.0.6      lifecycle_1.0.0   crayon_1.4.1      later_1.1.0.1    
[21] vctrs_0.3.6       promises_1.2.0.1  fs_1.5.0          glue_1.4.2       
[25] evaluate_0.14     rmarkdown_2.6     stringi_1.5.3     compiler_4.0.3   
[29] pillar_1.4.7      httpuv_1.5.5      pkgconfig_2.0.3