Last updated: 2022-02-10
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Knit directory: single-cell-topics/analysis/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| 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.