Last updated: 2021-11-16
Checks: 1 1
Knit directory: MS_lesions/
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Unstaged changes:
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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 (docs/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 | b9e43a8 | Macnair | 2021-10-23 | Update index |
| html | b9e43a8 | Macnair | 2021-10-23 | Update index |
| Rmd | 8a15881 | Macnair | 2021-10-18 |
Update index.Rmd with final MOFA results</td> </tr> <tr> <td>html</td> <td><a href="https://rawcdn.githack.com/wmacnair/MS_lesions/8a15881721c1904566ddafacc5e6e0e06412bd92/docs/index.html" target="_blank">8a15881</a></td> <td>Macnair</td> <td>2021-10-18</td> <td>Update index.Rmd with final MOFA results
|
| Rmd | 1552617 | Macnair | 2021-10-05 | Save MOFA genes to xls |
| html | 1552617 | Macnair | 2021-10-05 | Save MOFA genes to xls |
| Rmd | c1a0bff | Macnair | 2021-10-05 | Update GM MOFA with final metadata |
| html | c1a0bff | Macnair | 2021-10-05 | Update GM MOFA with final metadata |
| Rmd | c679b20 | Macnair | 2021-10-04 | Update index |
| html | c679b20 | Macnair | 2021-10-04 | Update index |
| Rmd | 391aef9 | Macnair | 2021-10-04 | Update index.html with new mofa analysis |
| html | 391aef9 | Macnair | 2021-10-04 | Update index.html with new mofa analysis |
| html | 62b9816 | Macnair | 2021-09-24 | Update index.html |
| Rmd | 9153b78 | Macnair | 2021-09-24 | Update index.Rmd |
| Rmd | dc248fa | Macnair | 2021-09-03 | Update index.html with links |
| html | 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 |
| html | 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 |
| html | 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 |
| html | 47b429a | Macnair | 2021-07-23 | Analyse ctrl GM vs WM, fine celltypes |
| Rmd | 903c384 | Macnair | 2021-07-22 | Update MOFA analysis |
| html | 903c384 | Macnair | 2021-07-22 | Update MOFA analysis |
| Rmd | 3a29e55 | Macnair | 2021-07-09 | Add MOFA patient analysis (WM only) |
| html | 3a29e55 | Macnair | 2021-07-09 | Add MOFA patient analysis (WM only) |
| Rmd | 1036875 | Macnair | 2021-07-02 | Add analysis of oligo-PCs via muscat |
| html | 1036875 | Macnair | 2021-07-02 | Add analysis of oligo-PCs via muscat |
| Rmd | 0ec42e1 | Macnair | 2021-06-20 | Update GSEA analysis, heatmaps, lesion-specific |
| html | 0ec42e1 | Macnair | 2021-06-20 | Update GSEA analysis, heatmaps, lesion-specific |
| Rmd | 856df8d | Macnair | 2021-06-15 | Update index with changes |
| html | 856df8d | Macnair | 2021-06-15 | Update index with changes |
| Rmd | 8ccd4e7 | Macnair | 2021-06-08 | Update muscat reports |
| html | 8ccd4e7 | Macnair | 2021-06-08 | Update muscat reports |
| Rmd | 5ab29c3 | Macnair | 2021-06-03 | typo in index.html |
| html | 5ab29c3 | Macnair | 2021-06-03 | typo in index.html |
| Rmd | bb0eebf | Macnair | 2021-06-03 | Updated index.html |
| html | bb0eebf | Macnair | 2021-06-03 | Updated index.html |
| Rmd | cfacffb | Macnair | 2021-05-27 | Updated index.html |
| html | cfacffb | Macnair | 2021-05-27 | Updated index.html |
| Rmd | 7f4198b | Macnair | 2021-05-26 | Updated index file |
| html | 7f4198b | Macnair | 2021-05-26 | Updated index file |
| Rmd | d4b022a | Macnair | 2021-05-21 | Fix typo in index.Rmd |
| html | d4b022a | Macnair | 2021-05-21 | Fix typo in index.Rmd |
| Rmd | 58205c2 | Macnair | 2021-05-21 | Update with random effects and markers |
| html | 58205c2 | Macnair | 2021-05-21 | Update with random effects and markers |
| html | 9852840 | Macnair | 2021-05-12 | Adding docs to repo for first time - massive! |
| 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 |
Manuscript
Shiny app links provided by Eneritz (last updated 2021-03-23, I think):
Cartana panel link
MOFA genes links (FINAL: last updated 2021-10-18)
SingleCellExperiment objectscDblFinder (last updated 2021-04-28)SampleQC (last updated 2021-04-28)conos (last updated 2021-04-29)SCCAF (last updated 2021-04-29)oNMF (last updated 2021-08-24)oNMF, pseudobulk version (last updated 2021-09-24)ANCOM-BC (FINAL: last updated 2021-11-16)ANCOM-BC and scCODA; 751k nuclei (last updated 2021-10-04)ANCOM-BC on clean cells (>= 1000 genes detected; 501k nuclei) and very clean cells (>= 2000 detected; 320k nuclei) (last updated 2021-06-03)scCODA tested with different reference celltypes (last updated 2021-03-19)muscat - lesion types in broad celltypes, WM only, patient as random effect (last updated 2021-06-19)muscat - lesion types in broad celltypes, GM only, patient as random effect (last updated 2021-06-19)muscat - lesion types in fine celltypes, WM only, patient as random effect (last updated 2021-06-19)muscat - lesion types in fine celltypes, GM only, patient as random effect (last updated 2021-06-19)muscat - ctrl GM vs WM in fine celltypes (last updated 2021-07-23)PAGA (last updated 2021-05-06)MOFA+ - WM (FINAL: last updated 2021-10-23)MOFA+ - GM (last updated 2021-10-23)These are generally checks against what we had before Christmas.
conos clustersSCCAF mergings