Last updated: 2022-05-28

Checks: 7 0

Knit directory: synovialscrnaseq/

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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 (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
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
Rmd e88c23e Reto Gerber 2021-07-12 add ambient RNA analysis
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
Rmd 480bf2b retogerber 2021-05-25 EC DA analysis
html 480bf2b retogerber 2021-05-25 EC DA analysis
html a301681 retogerber 2021-05-19 update complete analysis, new samples added
html 3447fde retogerber 2021-05-10 update DS analysis
Rmd 66841ec retogerber 2021-05-05 update complete DS analysis
html 66841ec retogerber 2021-05-05 update complete DS analysis
Rmd 53b76f8 retogerber 2021-05-04 add DS analysis for complete data
html 53b76f8 retogerber 2021-05-04 add DS analysis for complete data
Rmd b89cc83 retogerber 2021-04-09 allow hvg filter in iSEE
html b89cc83 retogerber 2021-04-09 allow hvg filter in iSEE
Rmd 5e1a17c retogerber 2021-04-06 add new iSEE script with filters
html 5e1a17c retogerber 2021-04-06 add new iSEE script with filters
Rmd 442fab0 retogerber 2021-03-29 update analysis workflow
html 442fab0 retogerber 2021-03-29 update analysis workflow
Rmd 08b6aaa retogerber 2021-03-25 update scripts, output, iSEE scripts, …
Rmd 7976045 retogerber 2021-03-08 add missing genes
html 7976045 retogerber 2021-03-08 add missing genes
Rmd 2b41f9a retogerber 2021-03-04 add ambient RNA Anaylsis, update iSEE script to install tidySingleCellExperiment
html 2b41f9a retogerber 2021-03-04 add ambient RNA Anaylsis, update iSEE script to install tidySingleCellExperiment
Rmd 6f9a2f8 retogerber 2021-02-25 add new data, rerun abundances
html 6f9a2f8 retogerber 2021-02-25 add new data, rerun abundances
Rmd cd11ff8 retogerber 2021-02-18 fix typo
html cd11ff8 retogerber 2021-02-18 fix typo
Rmd db8c4cb retogerber 2021-02-18 update index
html db8c4cb retogerber 2021-02-18 update index
Rmd ad8c83b retogerber 2021-02-11 update doc
html ad8c83b retogerber 2021-02-11 update doc
Rmd 35417ee retogerber 2021-02-11 update main page
html 35417ee retogerber 2021-02-11 update main page
Rmd 720ce81 retogerber 2021-02-04 add sample summary file
html 720ce81 retogerber 2021-02-04 add sample summary file
html 1430057 retogerber 2021-02-03 update index file
html 680e291 retogerber 2021-02-03 Build site.
Rmd 9cf5680 retogerber 2021-02-03 wflow_publish(“analysis/index.Rmd”)
Rmd a28e4c4 retogerber 2021-01-29 update website
html a28e4c4 retogerber 2021-01-29 update website
html 04c48dc retogerber 2021-01-29 add main website files
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: 2022-04-25 )
  3. HVG selection, Dimensionality reduction (Last modified: 2022-04-25 )
  4. Batch removal, Clustering
  5. Annotation + marker genes
  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=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=C             
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] magrittr_2.0.1  workflowr_1.6.2

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6        whisker_0.4       knitr_1.31        here_1.0.1       
 [5] R6_2.5.0          rlang_0.4.10      stringr_1.4.0     tools_4.0.3      
 [9] xfun_0.21         git2r_0.28.0      htmltools_0.5.1.1 ellipsis_0.3.1   
[13] yaml_2.2.1        digest_0.6.27     rprojroot_2.0.2   tibble_3.0.6     
[17] lifecycle_1.0.0   crayon_1.4.1      later_1.1.0.1     vctrs_0.3.6      
[21] promises_1.2.0.1  fs_1.5.0          glue_1.4.2        evaluate_0.14    
[25] rmarkdown_2.6     stringi_1.5.3     compiler_4.0.3    pillar_1.4.7     
[29] httpuv_1.5.5      pkgconfig_2.0.3