glmGamPoi: Fitting Gamma-Poisson Generalized Linear Models on Single Cell Count Data
Constantin Ahlmann-Eltze, Wolfgang Huber
Bioinformatics; 2020-12-09; doi: https://doi.org/10.1093/bioinformatics/btaa1009
This repository contains the code that was used to generate the figures for the paper that describes the glmGamPoi package.
The scripts that call glmGamPoi, DESeq2, and edgeR are in the benchmarks folder:
- run_benchmark-brain20k.R
- run_benchmark-mousegastrulation.R
- run_benchmark-pbmc4k.R
- run_benchmark-pbmc68k.R
- run_asymptotics_benchmark.R
- run_asymptotics_parameters_benchmark.R
Each script was run 5 times on a cluster and the results were extracted from the log files with the gather_XXX_results.Rmd scripts which are in the benchmarks folder as well.
The data folder contains the cleaned up tables that were used to produce the plots in the paper.
The plots were generated with the make_plots.Rmd script.