Last updated: 2022-04-26

Checks: 1 1

Knit directory: MS_lesions_snRNAseq/

This reproducible R Markdown analysis was created with workflowr (version 1.7.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.


The R Markdown file has unstaged changes. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

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The results in this page were generated with repository version 7edb2ec. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

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Ignored files:
    Ignored:    .Rprofile
    Ignored:    ._MS_lesions_snRNAseq.sublime-project
    Ignored:    MS_lesions_snRNAseq.sublime-project
    Ignored:    MS_lesions_snRNAseq.sublime-workspace
    Ignored:    analysis/ms12_markers_cache/
    Ignored:    analysis/ms99_manuscript_figures_cache/

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    Untracked:  analysis/.index.Rmd.swp

Unstaged changes:
    Modified:   analysis/index.Rmd

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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 7edb2ec Macnair 2022-04-26 Add source code link to front page
html 7edb2ec Macnair 2022-04-26 Add source code link to front page
Rmd 8f6077d Macnair 2022-04-06 Update index file
html 8f6077d Macnair 2022-04-06 Update index file
Rmd 9c3ce5a Macnair 2022-04-05 Remove all unnecessary files
Rmd 74935aa wmacnair 2022-03-06 Fix MOFA WM, update some plots
html 74935aa wmacnair 2022-03-06 Fix MOFA WM, update some plots
Rmd d83826d wmacnair 2022-01-27 Add pages summarizing DE results
html d83826d wmacnair 2022-01-27 Add pages summarizing DE results
Rmd ceedfd1 wmacnair 2022-01-17 Update index.html
html ceedfd1 wmacnair 2022-01-17 Update index.html
Rmd 93fa77e wmacnair 2022-01-05 Add superclean PAGA analysis
html 93fa77e wmacnair 2022-01-05 Add superclean PAGA analysis
Rmd 1a38d84 wmacnair 2021-12-17 Add initial version of file with all figures
html 1a38d84 wmacnair 2021-12-17 Add initial version of file with all figures
Rmd ff2b8fb wmacnair 2021-12-15 Update PAGA analysis, including colouring with ANCOM
html ff2b8fb wmacnair 2021-12-15 Update PAGA analysis, including colouring with ANCOM
Rmd 6706e1e wmacnair 2021-12-13 Update index to point to slim muscat results
html 6706e1e wmacnair 2021-12-13 Update index to point to slim muscat results
Rmd 9af1539 wmacnair 2021-12-13 Save GO terms associated with modules
html 9af1539 wmacnair 2021-12-13 Save GO terms associated with modules
Rmd 9ee5eee wmacnair 2021-12-08 Add oligo groupings to ms09_ancombc_mixed CLR plots
html 9ee5eee wmacnair 2021-12-08 Add oligo groupings to ms09_ancombc_mixed CLR plots
Rmd aa64e51 wmacnair 2021-12-06 Add comparison of abundances with Rowitch clusters
html aa64e51 wmacnair 2021-12-06 Add comparison of abundances with Rowitch clusters
Rmd 38f3fd8 wmacnair 2021-11-26 Update index with new figure slides link
html 38f3fd8 wmacnair 2021-11-26 Update index with new figure slides link
Rmd c8c9222 wmacnair 2021-11-26 Add fine type muscat links to index, update .gitignore
html c8c9222 wmacnair 2021-11-26 Add fine type muscat links to index, update .gitignore
Rmd e94e407 wmacnair 2021-11-25 Update index, also mofa code
html e94e407 wmacnair 2021-11-25 Update index, also mofa code
html 7fb1b95 wmacnair 2021-11-25 Host with GitLab.
Rmd afe32c6 Macnair 2021-11-16 Final version of ANCOM-BC analysis
Rmd b9e43a8 Macnair 2021-10-23 Update index
Rmd 8a15881 Macnair 2021-10-18 Update index.Rmd with final MOFA results`
Rmd 1552617 Macnair 2021-10-05 Save MOFA genes to xls
Rmd c1a0bff Macnair 2021-10-05 Update GM MOFA with final metadata
Rmd c679b20 Macnair 2021-10-04 Update index
Rmd 391aef9 Macnair 2021-10-04 Update index.html with new mofa analysis
Rmd 9153b78 Macnair 2021-09-24 Update index.Rmd
Rmd dc248fa Macnair 2021-09-03 Update index.html with links
Rmd 96d385e Macnair 2021-08-24 Update index.html, also a couple of minor tweaks
Rmd f60e5c1 Macnair 2021-08-03 Add astrocyte layer genes to ms12_markers
Rmd 47b429a Macnair 2021-07-23 Analyse ctrl GM vs WM, fine celltypes
Rmd 903c384 Macnair 2021-07-22 Update MOFA analysis
Rmd 3a29e55 Macnair 2021-07-09 Add MOFA patient analysis (WM only)
Rmd 1036875 Macnair 2021-07-02 Add analysis of oligo-PCs via muscat
Rmd 0ec42e1 Macnair 2021-06-20 Update GSEA analysis, heatmaps, lesion-specific
Rmd 856df8d Macnair 2021-06-15 Update index with changes
Rmd 8ccd4e7 Macnair 2021-06-08 Update muscat reports
Rmd 5ab29c3 Macnair 2021-06-03 typo in index.html
Rmd bb0eebf Macnair 2021-06-03 Updated index.html
Rmd cfacffb Macnair 2021-05-27 Updated index.html
Rmd 7f4198b Macnair 2021-05-26 Updated index file
Rmd d4b022a Macnair 2021-05-21 Fix typo in index.Rmd
Rmd 58205c2 Macnair 2021-05-21 Update with random effects and markers
Rmd eef8a1c Macnair 2021-04-29 Minor tweaks to allow rerunning on Roche servers
Rmd a6221cc wmacnair 2021-04-07 Giant update of recent work
Rmd d2a3b50 wmacnair 2021-02-10 Added admin files
Rmd 31fc587 wmacnair 2021-01-19 Initial commit of mainly blank repo

Overall figures

Pre-processing

Analysis