https://github.com/const-ae/glmgampoi-paper
Science Score: 26.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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✓DOI references
Found 2 DOI reference(s) in README -
○Academic publication links
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○Scientific vocabulary similarity
Low similarity (5.3%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: const-ae
- Language: HTML
- Default Branch: master
- Size: 32.6 MB
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- Stars: 1
- Watchers: 2
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Metadata Files
README.md
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 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
- runasymptoticsbenchmark.R
- runasymptoticsparameters_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.
Owner
- Name: Constantin
- Login: const-ae
- Kind: user
- Location: Heidelberg, Germany
- Company: EMBL
- Website: https://twitter.com/const_ae
- Repositories: 64
- Profile: https://github.com/const-ae
PhD Student, Biostats, R
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