Last updated: 2019-02-02
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File | Version | Author | Date | Message |
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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.
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.
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 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.
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