Last updated: 2019-09-05
workflowr checks: (Click a bullet for more information) ✔ R Markdown file: up-to-date
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.
✔ Repository version: e39d12e
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: .Rhistory
Ignored: .Rproj.user/
Ignored: .snakemake/
Ignored: data/molecules/
Ignored: data/reads/
Ignored: data/totals/
Ignored: data/verify/
Ignored: log/
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Untracked files:
Untracked: create-env.sh
Untracked: publish.bash
Untracked: snake.txt
Untracked: snakelog.out
Untracked: update-env.sh
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | e39d12e | John Blischak | 2019-09-05 | Update URLs on homepage. |
| html | d848f8e | Joyce Hsiao | 2019-02-12 | Build site. |
| Rmd | 391ed92 | Joyce Hsiao | 2019-02-12 | add John’s changes |
| Rmd | c4f411f | Joyce Hsiao | 2019-02-12 | move TOC |
| Rmd | 435d656 | Chiaowen Joyce Hsiao | 2019-02-12 | Merge branch ‘master’ into master |
| html | 435d656 | Chiaowen Joyce Hsiao | 2019-02-12 | Merge branch ‘master’ into master |
| Rmd | 9c05421 | Chiaowen Joyce Hsiao | 2019-02-12 | Merge pull request #57 from jdblischak/download |
| Rmd | 5b3779c | John Blischak | 2019-02-01 | Update workflowr to 1.0.1 with wflow_update(). |
| html | 9471094 | Joyce Hsiao | 2019-01-31 | Build site. |
| Rmd | 162f192 | Joyce Hsiao | 2019-01-31 | build homepage |
| html | 0544e3c | Joyce Hsiao | 2018-09-25 | Build site. |
| Rmd | 49ad6fd | Joyce Hsiao | 2018-09-25 | build homepage |
| html | e3e6dbf | Joyce Hsiao | 2018-07-17 | Build site. |
| Rmd | ff67833 | Joyce Hsiao | 2018-07-17 | update homepage |
| html | 453044f | Joyce Hsiao | 2018-07-12 | Build site. |
| Rmd | 1d8f214 | Joyce Hsiao | 2018-07-12 | update homepage |
| html | 6a46a6b | Joyce Hsiao | 2018-07-02 | Build site. |
| Rmd | efaea97 | Joyce Hsiao | 2018-07-02 | update homepage |
| html | c526f3f | Joyce Hsiao | 2018-06-29 | Build site. |
| Rmd | 78ce6d8 | Joyce Hsiao | 2018-06-29 | update homepage |
| html | 6a93de3 | Joyce Hsiao | 2018-06-28 | Build site. |
| Rmd | 9c0cc13 | Joyce Hsiao | 2018-06-28 | update hompage |
| html | 63fd7ff | Joyce Hsiao | 2018-06-21 | Build site. |
| Rmd | 5387a9c | Joyce Hsiao | 2018-06-21 | update hompage |
| html | 3dc9b89 | Joyce Hsiao | 2018-05-22 | Build site. |
| Rmd | b4cdf0a | Joyce Hsiao | 2018-05-22 | update homepage |
| html | dea875a | Joyce Hsiao | 2018-05-09 | Build site. |
| Rmd | fec5c5c | Joyce Hsiao | 2018-05-08 | update homepage |
| html | a625a22 | Joyce Hsiao | 2018-04-10 | Build site. |
| Rmd | 067340b | Joyce Hsiao | 2018-04-10 | update hompage |
| html | 688a3ba | Joyce Hsiao | 2018-03-15 | Build site. |
| Rmd | 0fc96fd | Joyce Hsiao | 2018-03-15 | re-organize homepage |
| html | 7205420 | Joyce Hsiao | 2018-03-09 | Build site. |
| Rmd | 94d2849 | Joyce Hsiao | 2018-03-09 | update hompage |
| html | e3ecf83 | Joyce Hsiao | 2018-02-26 | Build site. |
| Rmd | 920c732 | Joyce Hsiao | 2018-02-26 | update homepage |
| html | d2d3c37 | Joyce Hsiao | 2018-02-22 | Build site. |
| Rmd | e74c417 | Joyce Hsiao | 2018-02-22 | update homepage |
| html | 76f055a | Joyce Hsiao | 2018-02-14 | Build site. |
| Rmd | b04ee99 | Joyce Hsiao | 2018-02-14 | update homepage |
| html | 7d55333 | Joyce Hsiao | 2018-02-08 | Build site. |
| Rmd | af2ac8b | Joyce Hsiao | 2018-02-08 | update index |
| html | be18b2f | Joyce Hsiao | 2018-02-08 | Build site. |
| Rmd | e0ef1bd | Joyce Hsiao | 2018-02-08 | minor edits |
| html | 3ae09b6 | Joyce Hsiao | 2018-02-07 | Build site. |
| Rmd | 34c35b1 | Joyce Hsiao | 2018-02-07 | update homepage |
| html | 25e1a9f | Joyce Hsiao | 2018-02-01 | Build site. |
| Rmd | f6c8d2d | Joyce Hsiao | 2018-02-01 | update homepage |
| Rmd | 5a1ad9c | John Blischak | 2018-01-31 | Merge remote-tracking branch ‘jhsiao999/master’ |
| html | 9fb49f9 | Joyce Hsiao | 2018-01-31 | Build site. |
| Rmd | 36af913 | Joyce Hsiao | 2018-01-31 | update homepage |
| Rmd | 4b1a660 | pytung | 2018-01-31 | add analysis of PCA vs techinical factors |
| Rmd | 3909c4c | Joyce Hsiao | 2018-01-30 | update index |
| html | f422ce2 | Joyce Hsiao | 2018-01-25 | Build site. |
| Rmd | e5682e3 | Joyce Hsiao | 2018-01-25 | wflow_publish(“analysis/index.Rmd”) |
| html | bde6496 | Joyce Hsiao | 2017-12-21 | Build site. |
| Rmd | 556d50e | Joyce Hsiao | 2017-12-21 | update index |
| html | 913f2d1 | Joyce Hsiao | 2017-12-14 | Build site. |
| Rmd | 6fbaf59 | Joyce Hsiao | 2017-12-14 | wflow_publish(“analysis/index.Rmd”) |
| html | cff51ca | Joyce Hsiao | 2017-12-13 | Build site. |
| Rmd | 16d22e3 | Joyce Hsiao | 2017-12-13 | wflow_publish(“analysis/index.Rmd”) |
| html | 189df68 | Joyce Hsiao | 2017-12-12 | Build site. |
| Rmd | 95e8dda | Joyce Hsiao | 2017-12-12 | wflow_publish(“analysis/index.Rmd”) |
| Rmd | 6e3c938 | Joyce Hsiao | 2017-12-11 | Build site. |
| html | 3a4dd7c | Joyce Hsiao | 2017-12-01 | Build site. |
| Rmd | fbca340 | Joyce Hsiao | 2017-12-01 | update index |
| Rmd | ab2ad0c | John Blischak | 2017-11-29 | Fix merge conflict in index.Rmd. |
| html | ab2ad0c | John Blischak | 2017-11-29 | Fix merge conflict in index.Rmd. |
| Rmd | 0c360f7 | Chiaowen Hsiao | 2017-11-29 | update index |
| html | 0c360f7 | Chiaowen Hsiao | 2017-11-29 | update index |
| html | 4fcf7d1 | John Blischak | 2017-11-29 | Build site. |
| Rmd | 2582fb0 | John Blischak | 2017-11-29 | Investigate effect of C1 chip and individual on molecule conversion |
| html | 6898149 | John Blischak | 2017-11-29 | Build site. |
| Rmd | 3d5d193 | John Blischak | 2017-11-29 | Visualize sequencing depth per C1 chip. |
| Rmd | f41cb62 | Chiaowen Hsiao | 2017-11-20 | update index |
| html | f41cb62 | Chiaowen Hsiao | 2017-11-20 | update index |
| Rmd | cbaf910 | Chiaowen Hsiao | 2017-11-01 | add image QC follow-up to index page |
| html | cbaf910 | Chiaowen Hsiao | 2017-11-01 | add image QC follow-up to index page |
| Rmd | b238da6 | Chiaowen Hsiao | 2017-10-31 | update index |
| html | 620ad02 | Chiaowen Hsiao | 2017-10-31 | preliminary image anaysis, mainly QC |
| Rmd | bd252b5 | jhsiao999 | 2017-10-12 | update index |
| html | bd252b5 | jhsiao999 | 2017-10-12 | update index |
| html | f6b94c1 | jhsiao999 | 2017-10-12 | Build site. |
| Rmd | c8c2654 | jhsiao999 | 2017-10-12 | wflow_publish(all = TRUE) |
| Rmd | e7f5236 | John Blischak | 2017-10-11 | Start workflowr project. |
We used this site to collaborate and share our results. Please feel free to explore. The results that made it into the final paper are in the section Finalizing below. Here are some useful links:
Early analysis using trendfilter and evaluating model performance
Investigate the property and quality of the cell time labels derived from GFP and RFP: PVE of intensities by cell times, comparing PVEs by cell times from DAPI and FUCCI vs from FUCCI; comparing prediction before and after removing PC outliers (after is slightly better), and in different sets of genes.
Investigate the cyclical trends for each individual
Investigate the property of Seurat classes and cell time
Learning about correlation for circular response variable: some simulations to check its property and also relations with Fisher’s z transformation
We evaluated and pre-processed the results of image analysis as follows:
Why some gene symbols (genes) correspond to multiple Ensembl IDs?
I selected a set of cell cycle genes that belong to GO term Cell Cycle and looked at the overlap with the detected genes in our data.
Reproducing some QC analysis and making plots for a seminar talk
[Compile codes for the paper in ]
This reproducible R Markdown analysis was created with workflowr 1.0.1