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Last updated: 2019-02-02

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✔ Repository version: c7ecb56
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```
Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    BUSpaRse_notebooks.Rproj
    Ignored:    analysis/10xv2_cache/
    Ignored:    analysis/10xv3_cache/
    Ignored:    data/fastqs/
    Ignored:    data/hgmm_100_fastqs.tar
    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_hgmm100/
    Ignored:    output/out_hgmm1k/
    Ignored:    output/out_hgmm1k_v3/
```
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Expand here to see past versions:

File	Version	Author	Date	Message
html	85a5770	Lambda Moses	2018-12-14	Build site.
Rmd	ca1d6ce	Lambda Moses	2018-12-14	Clean up
html	6276894	Lambda Moses	2018-12-14	Build site.
html	1cc5f8a	Lambda Moses	2018-12-14	Build site.
Rmd	03c3319	Lambda Moses	2018-12-14	Changed site name
html	db70187	Lambda Moses	2018-12-14	Build site.
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. This package will be on Bioconductor soon.

Installation note for MacOS

In case you encounter this error during installation:

clang: error: unsupported option '-fopenmp'

This is what to do to resolve it:

This package contains compiled code, and a compiler that supports OpenMP is required to compile this package. However, the default clang that comes with MacOS does not support OpenMP. MacOS users using R 3.5 should download and install Clang 6.0 and gfortran 6.1 compilers from this webpage from CRAN, which has OpenMP enabled. R 3.5 no longer works with Clang 4, which was used for R 3.4.

Then, if the file ~/.R/Makevars does not exist, in the terminal, go to your home directory by cd, use mkdir .R to create the .R directory, and type vim Makevars to create and start editing the file. If it already exists, then type vim Makevars to edit it.

Alternatively, if you are uncomfortable with the command line, this can be done in RStudio. First use file.exists("~/.R/Makevars") to check if ~/.R/Makevars exists. Then use dir.exists("~/.R") to check that if the ~/.R directory exists. If it does not, then use dir.create("~/.R") to create the directory. Then use file.create("~/.R/Makevars") to create that file. Then navigate to that file in the Files pane in RStudio, open that file in RStudio, and edit it.

Add the following to the ~/.R/Makevars file:

CC=/usr/local/clang6/bin/clang
SHLIB_CXXLD=/usr/local/clang6/bin/clang++
CXX= /usr/local/clang6/bin/clang++  -Wall
CXX1X= /usr/local/clang6/bin/clang++
CXX98= /usr/local/clang6/bin/clang++
CXX11= /usr/local/clang6/bin/clang++
CXX14= /usr/local/clang6/bin/clang++
CXX17= /usr/local/clang6/bin/clang++
LDFLAGS=-L/usr/local/clang6/lib

Above is the default path where this Clang 6.0 is installed. Please change it if Clang 6.0 is installed in a custom path. This will tell R to use the Clang 6.0 from CRAN that has OpenMP enabled. Then restart the R session and reinstall this package.

Notebooks

Notebooks for Drop-seq and CEL-seq2 are coming soom.

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

This reproducible R Markdown analysis was created with workflowr 1.1.1