Last updated: 2024-02-19

Checks: 6 1

Knit directory: synovialscrnaseq/

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/index.Rmd) and HTML (public/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 58eeb06 Reto Gerber 2023-05-30 add new version
html 58eeb06 Reto Gerber 2023-05-30 add new version
html e786402 Reto Gerber 2022-05-28 update figures to final version of paper
html 0f8368f Reto Gerber 2022-05-20 update figures
Rmd 5a6aa2a Reto Gerber 2022-04-25 rerun with small resolution
html 5a6aa2a Reto Gerber 2022-04-25 rerun with small resolution
Rmd 3443cc6 Reto Gerber 2022-04-25 Update
html 3443cc6 Reto Gerber 2022-04-25 Update
html b5b139f Reto Gerber 2022-03-29 Update analysis
html 9133ed1 Reto Gerber 2022-03-04 update to v6
html 09496b7 Reto Gerber 2022-03-01 update clustering
Rmd 605da3e Reto Gerber 2022-01-20 update ec
html 605da3e Reto Gerber 2022-01-20 update ec
Rmd 27d00c3 Reto Gerber 2021-10-20 Add untracked files, update
html 27d00c3 Reto Gerber 2021-10-20 Add untracked files, update
Rmd d31dee0 Reto Gerber 2021-08-11 Add GSEA
html d31dee0 Reto Gerber 2021-08-11 Add GSEA
html f2e34e1 Reto Gerber 2021-07-29 Update navbar
html 222b0d1 Reto Gerber 2021-07-29 Update analysis to v5
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html e88c23e Reto Gerber 2021-07-12 add ambient RNA analysis
Rmd 6b4ed06 Reto Gerber 2021-07-01 Add new DS, update iSEE
html 6b4ed06 Reto Gerber 2021-07-01 Add new DS, update iSEE
html b10242c retogerber 2021-05-26 update ec DA
html a18fb61 retogerber 2021-05-26 workflow with no cultured and no low quality samples
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html 480bf2b retogerber 2021-05-25 EC DA analysis
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Rmd 0e7eabd retogerber 2021-01-05 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 including all Samples

  1. Swapped molecules and empty droplets check
  2. Preprocessing (Last modified: 2022-10-28 )
  3. HVG selection, Dimensionality reduction (Last modified: 2022-10-28 )
  4. Batch removal, Clustering
  5. Annotation + marker genes
  6. Trajectory analysis
  7. Figures

Analysis including all Samples + Stephenson + Wei

  1. Preprocessing (Last modified: 2022-12-19 )
  2. HVG selection, Dimensionality reduction (Last modified: 2022-12-19 )
  3. Batch removal, Clustering (Last modified: 2024-02-12 )
  4. Annotation + marker genes (Last modified: 2024-02-12 )
  5. Figures 1 (Last modified: 2024-02-12 )
  6. Figures 2 (Last modified: 2024-02-12 )

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