https://github.com/const-ae/glmgampoi-paper

https://github.com/const-ae/glmgampoi-paper

Last synced: 9 days ago
JSON representation

• Host: GitHub
• URL: https://github.com/const-ae/glmgampoi-paper
• Owner: const-ae
• Created: 2020-08-13T13:20:57.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2020-12-28T17:26:55.000Z (about 4 years ago)
• Last Synced: 2024-11-06T14:00:49.484Z (about 2 months ago)
• Language: HTML
• Size: 32.6 MB
• Stars: 1
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

README

        
# glmGamPoi-Paper

> 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](https://github.com/const-ae/glmGamPoi) package.

The scripts that call `glmGamPoi`, `DESeq2`, and `edgeR` are in the [benchmarks](https://github.com/const-ae/glmGamPoi-Paper/tree/master/benchmarks) folder:

* [run_benchmark-brain20k.R](https://github.com/const-ae/glmGamPoi-Paper/blob/master/benchmarks/run_benchmark-brain20k.R)

* [run_benchmark-mousegastrulation.R](https://github.com/const-ae/glmGamPoi-Paper/blob/master/benchmarks/run_benchmark-mousegastrulation.R)

* [run_benchmark-pbmc4k.R](https://github.com/const-ae/glmGamPoi-Paper/blob/master/benchmarks/run_benchmark-pbmc4k.R)

* [run_benchmark-pbmc68k.R](https://github.com/const-ae/glmGamPoi-Paper/blob/master/benchmarks/run_benchmark-pbmc68k.R)

* [run_asymptotics_benchmark.R](https://github.com/const-ae/glmGamPoi-Paper/blob/master/benchmarks/run_asymptotics_benchmark.R)

* [run_asymptotics_parameters_benchmark.R](https://github.com/const-ae/glmGamPoi-Paper/blob/master/benchmarks/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](https://github.com/const-ae/glmGamPoi-Paper/tree/master/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](http://htmlpreview.github.io/?https://github.com/const-ae/glmGamPoi-Paper/blob/master/make_plots.nb.html) script.