Last updated: 2025-06-16

Checks: 1 1

Knit directory: single-cell-jamboree/analysis/

This reproducible R Markdown analysis was created with workflowr (version 1.7.1). 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: b3f176c

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 b3f176c. 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: 


Untracked files:
    Untracked:  data/GSE156175_RAW/
    Untracked:  data/panc_cyto_lsa.Rdata
    Untracked:  data/panc_cyto_lsa_res/
    Untracked:  data/panc_cyto_lsa_tm_k12.rds

Unstaged changes:
    Modified:   analysis/index.Rmd

Staged changes:
    New:        analysis/pancreas_cytokine_mf_comparison.Rmd

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 b3f176c Eric Weine 2025-06-16 added initial clustering to index
html b3f176c Eric Weine 2025-06-16 added initial clustering to index
html 39b9a9c Peter Carbonetto 2025-06-09 Added a link to the overview page.
Rmd 71476db Peter Carbonetto 2025-06-09 wflow_publish("index.Rmd")
html d82311c Peter Carbonetto 2025-06-05 Added a link to the overview page.
Rmd f7eb98f Peter Carbonetto 2025-06-05 wflow_publish("index.Rmd")
html 7b87ef1 Peter Carbonetto 2025-06-04 Added a link to the overview page.
Rmd c2cfbec Peter Carbonetto 2025-06-04 wflow_publish("index.Rmd")
html 72059b6 Peter Carbonetto 2025-06-03 Added a link to the overview page.
Rmd ca9b2c6 Peter Carbonetto 2025-06-03 wflow_publish("index.Rmd")
html bc266b0 Peter Carbonetto 2025-02-18 Added another link to the overview page.
Rmd f51fb05 Peter Carbonetto 2025-02-18 workflowr::wflow_publish("index.Rmd", verbose = TRUE)
html a0e7a31 Ziang Zhang 2025-02-12 Build site.
Rmd b61d032 Ziang Zhang 2025-02-12 workflowr::wflow_publish("index.rmd")
html cdc88c3 Peter Carbonetto 2025-01-14 Added a link to the overview page.
Rmd e8c8a6c Peter Carbonetto 2025-01-14 workflowr::wflow_publish("index.Rmd")
Rmd 57b06fa Peter Carbonetto 2025-01-09 Removed temporary script temp.R.
html 3a11853 Peter Carbonetto 2025-01-09 Added link to the overview page.
Rmd f900873 Peter Carbonetto 2025-01-09 workflowr::wflow_publish("index.Rmd")
Rmd 1aca27c WD 2025-01-03 removing old work
html 52b8f2b Peter Carbonetto 2024-12-18 Added a link to the overview page.
Rmd 151ffdd Peter Carbonetto 2024-12-18 workflowr::wflow_publish("index.Rmd")
html 4ddf15d Peter Carbonetto 2024-12-18 Build site.
Rmd 772d36b Peter Carbonetto 2024-12-18 workflowr::wflow_publish("index.Rmd")
Rmd e264e5b Peter Carbonetto 2024-12-12 Created draft analysis in pancreas_celseq2.R; this will be incorporated into pancreas_another_look.Rmd.
html 0227b93 Peter Carbonetto 2024-12-12 Added link to the overview page.
Rmd ebc2e96 Peter Carbonetto 2024-12-12 workflowr::wflow_publish("index.Rmd")
html d1a51ec WD 2024-12-12 Build site.
Rmd 40ca4d0 WD 2024-12-12 adding NJ exploeration
html 1f511df Peter Carbonetto 2024-11-26 Changed one of the links.
Rmd fd2e11c Peter Carbonetto 2024-11-26 workflowr::wflow_publish("index.Rmd")
html b104b98 Peter Carbonetto 2024-11-21 Added link to overview page.
Rmd 6cc0dd9 Peter Carbonetto 2024-11-21 workflowr::wflow_publish("index.Rmd")
html 3cb6842 junmingguan 2024-11-17 Build site.
html 360f25c junmingguan 2024-11-17 Build site.
Rmd 14d98a1 junmingguan 2024-11-17 Change link for human brain cell COP analysis
html 3ed95ad Ziang Zhang 2024-11-15 Build site.
Rmd 9a3e3e2 Ziang Zhang 2024-11-15 workflowr::wflow_publish("analysis/index.Rmd")
Rmd 08af9f1 Peter Carbonetto 2024-11-06 Small fix to index.Rmd.
html 8ff4c1f Peter Carbonetto 2024-11-06 Ran workflowr::wflow_publish("index.Rmd").
Rmd 3c3db06 Peter Carbonetto 2024-11-06 Added link to overview page.
html 3d9da55 Peter Carbonetto 2024-11-05 Made a few fixes to Sagnik’s rmd.
html 04c5a1e Peter Carbonetto 2024-11-05 Added link to overview page.
Rmd 62acb47 Peter Carbonetto 2024-11-05 workflowr::wflow_publish("index.Rmd")
Rmd f6e58e0 Peter Carbonetto 2024-10-31 Small edit to index.Rmd.
html 4ae1a52 Peter Carbonetto 2024-10-31 Build site.
Rmd 5b0f28a Peter Carbonetto 2024-10-31 workflowr::wflow_publish("index.Rmd")
html e040f80 Peter Carbonetto 2024-10-31 Added link to the overview page.
Rmd 5362fbc Peter Carbonetto 2024-10-31 workflowr::wflow_publish("index.Rmd", verbose = TRUE)
html 766be29 Peter Carbonetto 2024-10-30 Small fix to the overview page.
Rmd 645a292 Peter Carbonetto 2024-10-30 workflowr::wflow_publish("index.Rmd")
html 8ff6c97 Peter Carbonetto 2024-10-30 Build site.
Rmd 214ec1a Peter Carbonetto 2024-10-30 workflowr::wflow_publish("index.Rmd")
html a3b945a Peter Carbonetto 2024-10-30 Build site.
Rmd 5479746 Peter Carbonetto 2024-10-30 workflowr::wflow_publish("index.Rmd")
html 528d5ef Peter Carbonetto 2024-10-30 First build of the pancreas workflowr page.
Rmd 6750e29 Peter Carbonetto 2024-10-30 workflowr::wflow_publish(c("pancreas.Rmd", "index.Rmd"))
Rmd c090d1d Peter Carbonetto 2024-10-30 Working on initial examination of pancreas data.
html 7638168 Peter Carbonetto 2024-10-21 Build site.
Rmd 6fcd079 Peter Carbonetto 2024-10-21 workflowr::wflow_publish("index.Rmd")
html 8a62d32 Peter Carbonetto 2024-10-21 Build the overview for the first time.
Rmd db49e71 Peter Carbonetto 2024-10-21 workflowr::wflow_publish("index.Rmd")
Rmd 401e597 Peter Carbonetto 2024-10-21 Ran wflow_start(".",name = "single-cell-jamboree",existing = TRUE,git = FALSE).

See here for an overview of the single-cell data sets.

The Human Cell Atlas is another potential source of interesting data sets.

Note that some of the processed data sets can be downloaded from Box via this link.

Analyses: