Last updated: 2022-01-27
Checks: 1 1
Knit directory: MS_lesions/
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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 |
---|---|---|---|---|
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 |
Writing
Figures
SingleCellExperiment
objectscDblFinder
(last updated 2021-04-28)SampleQC
(last updated 2021-04-28; too large to fit on website!)conos
(last updated 2021-04-29)SCCAF
(last updated 2021-04-29)oNMF
(last updated 2022-01-17)oNMF
, pseudobulk version (last updated 2021-09-24)ANCOM-BC
(FINAL: last updated 2021-12-13)MOFA+
- WM (FINAL: last updated 2021-10-23)MOFA+
- GM w layer PCs (FINAL: last updated 2021-11-25)PAGA
(FINAL: last updated 2021-12-14)PAGA
(w/ vv strict QC) (last updated 2022-01-05)These two pages are summaries and top hits for the DE analysis:
These are the fuller reports. To view these, you can either left-click then look for “open” and install BoxTools, or click right-click and download, then view locally.
These are generally checks against what we had before Christmas.
PAGA
(last updated 2021-05-06)conos
clustersSCCAF
mergingsShiny app links provided by Eneritz (last updated 2021-03-23, I think):
Cartana panel link
Modules outputs (FINAL: last updated 2021-12-13)
MOFA
genes links (FINAL: last updated 2021-11-25)