Last updated: 2020-10-03

Checks: 2 0

Knit directory: fucci-seq/analysis/

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.


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 6ce99e4. 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:


working directory clean

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 6ce99e4 John Blischak 2020-10-03 Update citation.
html 8aa2d71 jhsiao999 2019-09-17 Build site.
Rmd 05f661f jhsiao999 2019-09-17 wflow_publish("analysis/index.Rmd")
html 05f661f jhsiao999 2019-09-17 wflow_publish("analysis/index.Rmd")
html 237fdf1 John Blischak 2019-09-05 Build site.
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 435d656 GitHub 2019-02-12 Merge branch 'master' into master
html 984f9a9 Joyce Hsiao 2019-02-12 Build site.
Rmd c4f411f Joyce Hsiao 2019-02-12 move TOC
Rmd a0a3d31 John Blischak 2019-02-12 Document how to download data files. Close #56.
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 2018-05-09 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
Rmd af2ac8b John Blischak 2018-02-08 update index
html 7d55333 John Blischak 2018-02-08 Build site.
Rmd e0ef1bd John Blischak 2018-02-08 minor edits
html be18b2f John Blischak 2018-02-08 Build site.
Rmd 34c35b1 John Blischak 2018-02-08 update homepage
html 3ae09b6 John Blischak 2018-02-08 Build site.
html 2a026d4 Joyce Hsiao 2018-02-08 Build site.
Rmd 86e0a90 Joyce Hsiao 2018-02-08 update index
html 6991a4f Joyce Hsiao 2018-02-08 Build site.
Rmd e4747bc Joyce Hsiao 2018-02-08 minor edits
html 59d28df Joyce Hsiao 2018-02-07 Build site.
Rmd 5991f68 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 2017-12-02 Build site.
Rmd fbca340 Joyce Hsiao 2017-12-02 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:

Analysis

Supervised method learning: finalizing on data holiding out validation samples

Supervised method learning: building the analysis approach

Approaches to fitting cyclical trend in gene expression data

Cell cycle signal in gene expression data

  1. We investigated cell cycle signals in the sequencing data alone.
  2. We then assign categorical labels of cell cycle and explored the expresson profiles of these categories.
  3. We inferred an angle for each cell on a unit circle using FUCCI intensities alone.
  4. I used nonparametric methods to identify genes that may be cyclical along cell cycle phases.
    • Fit smash and kernel regression on circular variables on a subset of genes with detection rate > .8.
    • Fit trendfilter on a subset of genes (5) that are observed (visually) to have cyclical pattern. trendfilter is robust to small proportion of undetected cells, approx 2 or 3%. In cases of simulation when increasing proportion of undetected cells to 20%, we observed a flat line in gene expression for genes previously identified to tend to a cyclical pattern.
    • Next, we fit trendfilter on all genes after transforming the data to follow standard normal distribution, permutation-based p-values for PVE are used to select 101 significant cyclical genes.
  5. Additional analysis done to identify top cyclical genes in each individual. The top 5 are not shared across the six individuals. Results

RNA-seq data preprcessing

  1. The first step in preprocessing RNA-seq data consists of QC and filtering.
  2. We then analyzed and corrected for batch effect due to C1 plate in the sequencing data

Microscopy image analysis

We evaluated and pre-processed the results of image analysis as follows:

  1. We visually inspect images deteced to have none or more than one nucleus. For cases that are inconsistent with visual inspection, we correct the number of nuclei detected.
  2. We applied background correction to the intensity measurements of GFP, RFP and DAPI based on the following analyses.
  3. We analyzed intensity variation across individuals and batches and considers approaches for removing batch effects in the data.
  4. We investigated the cell time estimates based on FUCCI intensities.