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Last updated: 2018-12-14

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✔ 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: b67fc92
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:    BUSpaRse_notebooks.Rproj
    Ignored:    analysis/10xv2_cache/
    Ignored:    data/fastqs/
    Ignored:    data/hgmm_1k_fastqs.tar
    Ignored:    data/hgmm_1k_v3_fastqs.tar
    Ignored:    data/hgmm_1k_v3_fastqs/
    Ignored:    data/hs_cdna.fa.gz
    Ignored:    data/mm_cdna.fa.gz
    Ignored:    data/whitelist_v2.txt
    Ignored:    data/whitelist_v3.txt.gz
    Ignored:    output/hs_mm_tr_index.idx
    Ignored:    output/out_hgmm1k/
    Ignored:    output/out_hgmm1k_v3/

Untracked files:
    Untracked:  analysis/10xv3.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.

Expand here to see past versions:

File	Version	Author	Date	Message
Rmd	b67fc92	Lambda Moses	2018-12-14	Added 10xv3 notebook and further elaboration to 10xv2 notebook
html	064264a	Lambda Moses	2018-12-14	Build site.
Rmd	d5d64e9	Lambda Moses	2018-12-14	Added installation instruction
html	f5616a8	Lambda Moses	2018-12-14	Build site.
Rmd	0dc76a9	Lambda Moses	2018-12-14	Changed to new url
html	540134b	Lambda Moses	2018-12-14	Build site.
Rmd	e40da79	Lambda Moses	2018-12-14	Changed URL as this repo is transferred to BUStools
html	fff442d	Lambda Moses	2018-12-14	Build site.
Rmd	695e202	Lambda Moses	2018-12-14	Changed name to BUSpaRse
html	9209390	Lambda Moses	2018-12-14	Update website
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 BUSpaRse R package.

Installation of BUSpaRse

You can install BUSpaRse with:

if (!require(devtools)) install.packages("devtools")
devtools::install_github("BUStools/BUSpaRse")

This is work in progress. I’m trying to get this package to Bioconductor.

Notebooks

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