Last updated: 2022-03-11
Checks: 2 0
Knit directory: single-cell-topics/analysis/
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.
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
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 dd4b21a. 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: data/droplet.RData
Ignored: data/pbmc_purified.RData
Ignored: output/droplet/diff-count-droplet.RData
Ignored: output/droplet/fits-droplet.RData
Ignored: output/droplet/rds/
Ignored: output/pbmc-purified/fits-pbmc-purified.RData
Ignored: output/pbmc-purified/rds/
Ignored: output/sims/
Untracked files:
Untracked: analysis/de_analysis_detailed_look_cache/
Untracked: analysis/de_analysis_detailed_look_more_cache/
Untracked: plots/
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 | dd4b21a | Peter Carbonetto | 2022-03-11 | Removed analyses relating to pulseseq data. |
| html | 271518c | Peter Carbonetto | 2022-02-10 | Added another link to overview page. |
| Rmd | ad0daee | Peter Carbonetto | 2022-02-10 | workflowr::wflow_publish(“index.Rmd”) |
| html | efaf6e2 | Peter Carbonetto | 2022-02-10 | Added link to overview page. |
| Rmd | 43f7a9e | Peter Carbonetto | 2022-02-10 | workflowr::wflow_publish(“index.Rmd”) |
| html | e0bb26d | Peter Carbonetto | 2022-01-30 | Fixed link in overview page. |
| Rmd | 618a9e2 | Peter Carbonetto | 2022-01-30 | workflowr::wflow_publish(“index.Rmd”) |
| html | 65f4299 | Peter Carbonetto | 2022-01-28 | Build site. |
| Rmd | 2f6833f | Peter Carbonetto | 2022-01-28 | workflowr::wflow_publish(“index.Rmd”) |
| html | 9a0206c | Peter Carbonetto | 2022-01-28 | Updated the overview page. |
| Rmd | 398385c | Peter Carbonetto | 2022-01-28 | workflowr::wflow_publish(“index.Rmd”) |
| html | 2d18711 | Peter Carbonetto | 2022-01-05 | Added a couple links to the overview page. |
| Rmd | 625f08a | Peter Carbonetto | 2022-01-05 | workflowr::wflow_publish(“index.Rmd”) |
| Rmd | 283c7ba | Peter Carbonetto | 2022-01-05 | Working on de_analysis_mast_deseq2 R Markdown. |
| html | f60a975 | Peter Carbonetto | 2022-01-05 | Fixed the link. |
| Rmd | be88eab | Peter Carbonetto | 2022-01-05 | workflowr::wflow_publish(“index.Rmd”) |
| html | e164b8f | Peter Carbonetto | 2022-01-05 | Added link to overview page. |
| Rmd | 3de0e0c | Peter Carbonetto | 2022-01-05 | workflowr::wflow_publish(“index.Rmd”) |
| html | 4064c23 | Peter Carbonetto | 2021-12-30 | Updated links in overview page. |
| Rmd | 7d816c0 | Peter Carbonetto | 2021-12-30 | workflowr::wflow_publish(“index.Rmd”, verbose = TRUE) |
| html | b690ec8 | Peter Carbonetto | 2021-12-30 | Build site. |
| Rmd | b202b68 | Peter Carbonetto | 2021-12-30 | Removed link from overview page. |
| html | faf7ae8 | Peter Carbonetto | 2021-12-01 | Removed a couple links from the overview page. |
| Rmd | 4001127 | Peter Carbonetto | 2021-12-01 | Removed the clustering and assessment of fits for the 68k pbmc data. |
| html | 7bb3077 | Peter Carbonetto | 2021-11-30 | Updated link on overview page. |
| Rmd | 54d2d19 | Peter Carbonetto | 2021-11-30 | Removed prepare_68k_pbmc analysis. |
| html | 2befadb | Peter Carbonetto | 2021-11-08 | Added link to overview page. |
| Rmd | 71e267d | Peter Carbonetto | 2021-11-08 | workflowr::wflow_publish(“index.Rmd”) |
| html | f2cd3c7 | Peter Carbonetto | 2021-10-20 | Fixed link in overview page. |
| Rmd | 27b2d08 | Peter Carbonetto | 2021-10-20 | workflowr::wflow_publish(“index.Rmd”) |
| html | ed35cd9 | Peter Carbonetto | 2021-10-18 | Added link to overview page. |
| Rmd | 681296e | Peter Carbonetto | 2021-10-18 | workflowr::wflow_publish(“index.Rmd”) |
| html | da1a3c6 | Peter Carbonetto | 2021-10-09 | Added link to home page. |
| Rmd | 3be2035 | Peter Carbonetto | 2021-10-09 | workflowr::wflow_publish(“index.Rmd”) |
| Rmd | 4e298d9 | Peter Carbonetto | 2021-01-06 | Small edit to overview page. |
| html | 5303229 | Peter Carbonetto | 2021-01-04 | Made a few revisions to the overview page. |
| Rmd | b6f77c1 | Peter Carbonetto | 2021-01-04 | workflowr::wflow_publish(“index.Rmd”) |
| Rmd | 5b1983f | Peter Carbonetto | 2021-01-03 | A few minor changes to the analysis of the purified PBMC data. |
| html | 134ea78 | Peter Carbonetto | 2021-01-03 | Updated the overview page. |
| Rmd | 83151f0 | Peter Carbonetto | 2021-01-03 | workflowr::wflow_publish(“index.Rmd”) |
| Rmd | 56b9684 | Peter Carbonetto | 2020-12-29 | Added new section to overview page on single-cell likelihoods. |
| Rmd | 0ef8a20 | Peter Carbonetto | 2020-11-26 | Working on solving purified PBMC ‘mysteries’. |
| html | a9eece0 | Peter Carbonetto | 2020-11-13 | Updated the overview page. |
| Rmd | 672e1e3 | Peter Carbonetto | 2020-11-13 | workflowr::wflow_publish(“index.Rmd”) |
| Rmd | dc98449 | Peter Carbonetto | 2020-11-11 | Added B-cells cluster to clusters_purified_pbmc.R. |
| Rmd | 5e57ced | Peter Carbonetto | 2020-10-03 | Working on plots highlighting substructure in T+N cluster. |
| Rmd | 29e727c | Peter Carbonetto | 2020-10-01 | Minor edits. |
| Rmd | a9ae3b4 | Peter Carbonetto | 2020-09-24 | Working on new analysis, diff_count_droplet.Rmd. |
| html | 71300ae | Peter Carbonetto | 2020-09-24 | Added links to overview page. |
| Rmd | ab22824 | Peter Carbonetto | 2020-09-24 | workflowr::wflow_publish(“index.Rmd”) |
| html | 485628f | Peter Carbonetto | 2020-09-21 | Revised overview page. |
| Rmd | dd9d050 | Peter Carbonetto | 2020-09-21 | workflowr::wflow_publish(“index.Rmd”) |
| Rmd | 04e1761 | Peter Carbonetto | 2020-09-19 | A couple minor edits to the R Markdown. |
| html | 4820962 | Peter Carbonetto | 2020-09-18 | Added a couple links to overview page. |
| Rmd | 979b217 | Peter Carbonetto | 2020-09-18 | workflowr::wflow_publish(“index.Rmd”) |
| html | 279f62d | Peter Carbonetto | 2020-09-11 | Fixed link in overview page. |
| Rmd | 19f5623 | Peter Carbonetto | 2020-09-11 | workflowr::wflow_publish(“index.Rmd”) |
| html | 0208a08 | Peter Carbonetto | 2020-09-11 | Added link to overview page. |
| Rmd | d32e14c | Peter Carbonetto | 2020-09-11 | workflowr::wflow_publish(“index.Rmd”) |
| Rmd | 00e8002 | Peter Carbonetto | 2020-08-27 | Implemented new function pca_hex_plot in plots.R. |
| html | e77420b | Peter Carbonetto | 2020-08-25 | Added “source” button to navbar. |
| Rmd | 66bbdf4 | Peter Carbonetto | 2020-08-18 | Implemented functions basic_pca_plot and pca_plot_with_labels in plots.R. |
| html | 64b881d | Peter Carbonetto | 2020-08-18 | Updated links in overview page. |
| Rmd | 61917ad | Peter Carbonetto | 2020-08-18 | Working on new analysis, plots_tracheal_epithelium.Rmd. |
| html | 7b10d81 | Peter Carbonetto | 2020-08-10 | A couple minor edits to the overview page. |
| Rmd | 2b9f856 | Peter Carbonetto | 2020-08-10 | wflow_publish(“index.Rmd”) |
| html | 94e55ae | Peter Carbonetto | 2020-08-10 | Updated overview page. |
| Rmd | bd72e7d | Peter Carbonetto | 2020-08-10 | wflow_publish(“index.Rmd”) |
| html | c652099 | Peter Carbonetto | 2020-07-28 | Added some explanatory text to the overview page. |
| Rmd | 7d5e9c8 | Peter Carbonetto | 2020-07-28 | wflow_publish(“index.Rmd”, view = FALSE, verbose = TRUE) |
| html | e8da766 | Peter Carbonetto | 2020-07-26 | Added more links to overview page. |
| Rmd | 3136222 | Peter Carbonetto | 2020-07-26 | wflow_publish(“index.Rmd”) |
| html | a42d6cc | Peter Carbonetto | 2020-07-26 | Fixed links in overview page. |
| Rmd | 67d1667 | Peter Carbonetto | 2020-07-26 | wflow_publish(“index.Rmd”) |
| html | 15b3a57 | Peter Carbonetto | 2020-07-26 | Added links to overview page. |
| Rmd | be55916 | Peter Carbonetto | 2020-07-26 | wflow_publish(“index.Rmd”) |
| html | c46e2fe | Peter Carbonetto | 2020-07-26 | Build home page and populated docs folder. |
| Rmd | 8890f6b | Peter Carbonetto | 2020-07-26 | wflow_publish(“index.Rmd”) |
| Rmd | 8237842 | Peter Carbonetto | 2020-07-26 | Added workflowr files. |
In these pages, we assess the new topic-model-based methods for differential expression analysis, and compare with MAST and DESeq2.
For a more systematic evaluation in multiple simulated data sets, see these pages:
These pages detail the steps taken to prepare the single-cell RNA-seq data sets for topic modeling analysis.
In these pages, we compare the quality of the Poisson NMF fits with different updates (EM, CCD, SCD, with and without extrapolation), and with different settings for \(K\).
In these pages, we identify clusters of cells from the mixture proportions.
In these pages, we annotate topics to determine their biological relevance.