Last updated: 2018-12-02
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: f5dda86
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: .Rproj.user/
Ignored: analysis/Quality_metrics_cache/
Ignored: analysis/figure/
Unstaged changes:
Modified: analysis/Quality_metrics.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.
File | Version | Author | Date | Message |
---|---|---|---|---|
html | 9f8ba8d | szhao06 | 2018-12-02 | qc |
html | c206c9d | szhao06 | 2018-12-01 | qc |
Rmd | fdd5647 | szhao06 | 2018-12-01 | qc |
html | fdd5647 | szhao06 | 2018-12-01 | qc |
html | 6360503 | simingz | 2018-11-20 | Build site. |
Rmd | 8be64d0 | simingz | 2018-11-20 | First |
Rmd | fe55f5d | simingz | 2018-11-19 | Start workflowr project. |
Exploratory Analysis & DESeq2 from Alan (11/07/2018)
Exploratory Analysis from Siwei (11/19/2018)
In this workflow, I show how to process the raw FastQ files into count matrices representing UMI. We use the CellRanger toolkit to perform the processing. Then, we load the UMI matrices into R and perform exploratory analysis. We find that 2200+ cells have exactly 1 guide RNA and ~400 cells have zero. For the top expressed guide RNA, we perform differential expression analysis using DESeq2.
This reproducible R Markdown analysis was created with workflowr 1.1.1