Last updated: 2018-12-14

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: 37238e5

  Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.
  
  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:    .Rhistory
      Ignored:    .Rproj.user/
      Ignored:    data/fastqs/
      Ignored:    data/hgmm_1k_fastqs.tar
      Ignored:    data/hs_cdna.fa.gz
      Ignored:    data/mm_cdna.fa.gz
      Ignored:    data/whitelist_v2.txt
      Ignored:    output/hs_mm_tr_index.idx
      Ignored:    output/out_hgmm1k/
  
  Untracked files:
      Untracked:  analysis/10xv2_cache/
  
  

  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.

Expand here to see past versions:

File	Version	Author	Date	Message
Rmd	37238e5	Lambda Moses	2018-12-14	Link to this GitHub repo on the website
html	2da3b35	Lambda Moses	2018-12-14	Build site.
Rmd	55164fb	Lambda Moses	2018-12-14	Start workflowr project.

---

This repository has example notebooks that demonstrate how to go from fastq files to sparse matrices for scRNA-seq data from start to end. To run the notebooks, please install kallisto, bustools, and the BUStoolsR R package.

1. 10x v2 chemistry - 1k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells
2. 10x v3 chemistry - 1k 1:1 Mixture of Fresh Frozen Human (HEK293T) and Mouse (NIH3T3) Cells (coming soon)

If you have problems with the notebooks, or have questions about them, please go to the GitHub repo of this website.

---

This reproducible R Markdown analysis was created with workflowr 1.1.1

---