Last updated: 2021-11-25

Checks: 1 1

Knit directory: MS_lesions/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: uncommitted changes

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.

Repository version: fe25fbf

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version fe25fbf. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated: 


Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    .Rprofile
    Ignored:    .Rproj.user/
    Ignored:    ._MS_lesions.sublime-project
    Ignored:    .log/
    Ignored:    MS_lesions.sublime-project
    Ignored:    MS_lesions.sublime-workspace
    Ignored:    analysis/.__site.yml
    Ignored:    analysis/fig_muscat_cache/
    Ignored:    analysis/ms02_doublet_id_cache/
    Ignored:    analysis/ms03_SampleQC_cache/
    Ignored:    analysis/ms04_conos_cache/
    Ignored:    analysis/ms05_splitting_cache/
    Ignored:    analysis/ms06_sccaf_cache/
    Ignored:    analysis/ms07_soup_cache/
    Ignored:    analysis/ms08_modules_cache/
    Ignored:    analysis/ms08_modules_pseudobulk_cache/
    Ignored:    analysis/ms09_ancombc_cache/
    Ignored:    analysis/ms09_ancombc_clean_1e3_cache/
    Ignored:    analysis/ms09_ancombc_clean_2e3_cache/
    Ignored:    analysis/ms09_ancombc_mixed_cache/
    Ignored:    analysis/ms10_muscat_run01_cache/
    Ignored:    analysis/ms10_muscat_run02_cache/
    Ignored:    analysis/ms10_muscat_template_broad_cache/
    Ignored:    analysis/ms10_muscat_template_fine_cache/
    Ignored:    analysis/ms11_paga_cache/
    Ignored:    analysis/ms12_markers_cache/
    Ignored:    analysis/ms13_labelling_cache/
    Ignored:    analysis/ms14_lesions_cache/
    Ignored:    analysis/ms15_mofa_sample_gm_cache/
    Ignored:    analysis/ms15_mofa_sample_gm_final_meta_cache/
    Ignored:    analysis/ms15_mofa_sample_gm_superclean_cache/
    Ignored:    analysis/ms15_mofa_sample_gm_w_layers_final_meta_cache/
    Ignored:    analysis/ms15_mofa_sample_wm_cache/
    Ignored:    analysis/ms15_mofa_sample_wm_final_meta_cache/
    Ignored:    analysis/ms15_mofa_sample_wm_new_meta_cache/
    Ignored:    analysis/ms15_mofa_sample_wm_superclean_cache/
    Ignored:    analysis/ms15_patients_cache/
    Ignored:    analysis/ms15_patients_gm_cache/
    Ignored:    analysis/ms15_patients_sample_level_cache/
    Ignored:    analysis/ms15_patients_w_ms_cache/
    Ignored:    analysis/supp06_sccaf_cache/
    Ignored:    analysis/supp07_superclean_check_cache/
    Ignored:    analysis/supp09_ancombc_cache/
    Ignored:    analysis/supp09_ancombc_mixed_cache/
    Ignored:    analysis/supp09_ancombc_superclean_cache/
    Ignored:    analysis/supp10_muscat_cache/
    Ignored:    analysis/supp10_muscat_ctrl_gm_vs_wm_cache/
    Ignored:    analysis/supp10_muscat_gm_layers_effects_cache/
    Ignored:    analysis/supp10_muscat_heatmaps_cache/
    Ignored:    analysis/supp10_muscat_olg_pc1_cache/
    Ignored:    analysis/supp10_muscat_olg_pc2_cache/
    Ignored:    analysis/supp10_muscat_olg_pc_cache/
    Ignored:    analysis/supp10_muscat_regression_cache/
    Ignored:    analysis/supp10_muscat_soup_cache/
    Ignored:    analysis/supp10_muscat_soup_mito_cache/
    Ignored:    code/._ms10_muscat_fns_recover.R
    Ignored:    code/.recovery/
    Ignored:    code/jobs/._muscat_run09_2021-10-11.slurm
    Ignored:    code/muscat_plan.txt
    Ignored:    data/
    Ignored:    figures/
    Ignored:    output/
    Ignored:    tmp/

Untracked files:
    Untracked:  analysis/supp09_ancombc_superclean.Rmd
    Untracked:  docs/

Unstaged changes:
    Modified:   analysis/index.Rmd
    Modified:   analysis/ms14_lesions.Rmd
    Modified:   analysis/ms15_mofa_sample_gm_w_layers_final_meta.Rmd
    Modified:   analysis/ms15_mofa_sample_wm_final_meta.Rmd
    Modified:   analysis/ms15_mofa_sample_wm_superclean.Rmd
    Modified:   analysis/supp07_superclean_check.Rmd
    Modified:   code/dev_edger_on_mofa_20210804.R
    Modified:   code/ms10_muscat_fns.R
    Modified:   code/ms10_muscat_runs.R
    Modified:   code/ms14_lesions.R
    Modified:   code/ms15_mofa.R
    Modified:   code/supp10_muscat.R

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 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

Overview

Pre-processing

Analysis

Pseudobulk differential expression outputs

To view these, you can either left-click then look for “open” and install BoxTools, or click right-click and download, then view locally.

Checks / additional analysis (not currently intended to be included in the paper)

These are generally checks against what we had before Christmas.