This is a Github repository to accompany the paper:
Risso D, Purvis L, Fletcher R, Das D, Ngai J, Dudoit S, Purdom E (2018) "clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets" PLoS Comput Biol. 2018 Sep 4;14(9):e1006378 http://dx.plos.org/10.1371/journal.pcbi.1006378
How to Reproduce the analysis
The provided make file will allow you to recreate the analysis in the paper from scratch. This code includes downloading the data from GEO.
You should first have R installed and the necessary packages installed: (
Then type the following commands:
Note that this is quite computationally intensive, and runs on parallel cores (by default the value defined by the environment variable
SLURM_CPUS_PER_TASK or 6 if such a value is missing). So it should only be run from scratch in a setting appropriate to this.
Using the provided intermediate results (quicker)
To have quicker access to the data and results, we also provide (via
.rda files that are the result of the output of downloading the data, and the
RSEC command (see https://git-lfs.github.com/ for instructions on
git lfs and how to download these files). They are saved under the directory
To be able to run the above make command, and not have to rerun the computationally intensive commands, you must make the following changes:
Move (or copy) the directory
Edit the file
OEAnalysis.Rso that the line
now reads as
After these changes you should be able to run the above make command,
With these settings, the scripts should be able to run on a laptop relatively quickly.