Data and analysis for the paper "Splatter: Simulation of Single-cell RNA sequencing data".
additional- Supplementary figures and files
analysis- Analysis files and output
data- Input data files
figures- Figures used in the main paper
output- Additional intermediate files
R- R functions used in analysis
Data files used in the analysis are available in the
data.tar.gz file. This
file should be extracted to
data before attempting to run any of the analysis.
tar -xzvf data.tar.gz
After extraction the
data directory will contain the following files:
datasets.txt- Metadata about the various datasets
Camp.txt- The Camp dataset
Engel.tsv- The Engel dataset
Klein.csv- The Klein dataset
Tung.txt- The Tung dataset
Zeisel.txt- The Zeisel dataset
The code for completing the analysis shown in the paper is provided as the following Rmarkdown files in the analysis directory:
simulations.Rmd- Some examples of Splat simulations.
performance.Rmd- Processing time benchmarking.
datasets.Rmd- Comparison of simulations based on various datasets.
clustering.Rmd- Example evaluation of the SC3 clustering method.
supplementary.Rmd- Supplementary figures.
There are two additional Rmd files which are rendered via
additional_figures.Rmd which combines the additional figures into a
single PDF and
sessionInfo.Rmd which outputs the details of all the packages
used during the analysis.
Running the analysis files will produce figure files in the
additional directories as well as data files in the
Please be aware that some of the analysis (particularly
large amounts of resources (processing, memory, time) and may require slight
modifications to run in your environment.
This directory contains the following functions used in the analysis:
loadDataset- Takes a row from
datasets.txtand the path to the data files then returns an expression matrix for that dataset
simData- Takes a counts matrix, estimates parameters and simulates data using various models
testGenesGoF- Test the goodness of fit for each gene with regards to various distributions
chrRound- Rounds a number for presentation, converting it to a string
logistic- Implementation of the logistic function
mcri.palettes- List of colour palettes used for some plots
mcriPalette- Returns colour palette of particular size