https://github.com/const-ae/transformgampoi-paper
Science Score: 23.0%
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
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✓Academic publication links
Links to: nature.com, zenodo.org -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (8.5%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: const-ae
- License: gpl-3.0
- Language: HTML
- Default Branch: master
- Size: 167 MB
Statistics
- Stars: 28
- Watchers: 3
- Forks: 7
- Open Issues: 4
- Releases: 3
Metadata Files
README.md
Online Supplement of Comparison of Transformations for Single-Cell RNA-Seq Data
This repository contains the code to generate the figures of our paper 'Comparison of Transformations for Single-Cell RNA-Seq Data' in Nature Methods https://www.nature.com/articles/s41592-023-01814-1.
The accompanying R package transformGamPoi is available via Bioconductor or at https://github.com/const-ae/transformGamPoi.
At https://shiny-portal.embl.de/shinyapps/app/08single-celltransformation_benchmark, we provide an interactive website to explore the benchmark results. The underlying source code is available at https://github.com/const-ae/transformGamPoi-ShinyApp.
Repository content
The repository is organized into four folders. The root directory contains some additional files for documentation and data plumbing purposes.
- benchmark contains the infrastructure for our benchmark of 22 different transformation methods. The job_overview.yaml is a declarative specification of all the parameter combinations (more than 58,000) that we benchmarked. The renv.lock file contains detailed information about each R package that was used in the benchmark using the
renvsystem. - notebooks contains the Rmd scripts to generate the plots shown in the manuscript. Links to the rendered HTML notebooks are below
- illustrations and output contain the figures
Code to generate figures
- Figure 1: Conceptual differences between variance-stabilizing transformations
- Figure 2: Benchmark results
- Figure 3: Computational expense
* Figure 4: Comparison of selected transformations
- plotsizefactoreffectondimreduction.Rmd generates Extended Data Fig. S1.
- plotvariancestabilization_results.Rmd generates Extended Data Fig. S2.
- plotbimodalgene_histograms.Rmd generates Extended Data Fig. S3.
- plotdatasetstructure.Rmd generates Suppl. Figs. S1, Extended Data Fig. S5, and Suppl. Tabl. S1.
- plotbenchmarkresults.Rmd generates Extended Data Figs. S6, S7, in addition to Fig. 2 and 3.
- plotdeepsequenced_overlap.Rmd generates Extended Data Fig. S8.
- plotclusteringresults.Rmd generates Extended Data Fig. S9.
- plotstratifiedperformance.Rmd generates Extended Data Figs. S10.
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
GitHub Events
Total
- Issues event: 2
- Watch event: 1
- Issue comment event: 1
Last Year
- Issues event: 2
- Watch event: 1
- Issue comment event: 1
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 9
- Total pull requests: 2
- Average time to close issues: 7 days
- Average time to close pull requests: about 19 hours
- Total issue authors: 6
- Total pull request authors: 2
- Average comments per issue: 3.33
- Average comments per pull request: 2.5
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 2
- Pull request authors: 0
- Average comments per issue: 1.5
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- kuang-da (3)
- cakeinspace (2)
- AdotaLover (1)
- Minhui-Chen (1)
- mjcasy (1)
- shashwatsahay (1)
Pull Request Authors
- HelloWorldLTY (1)
- const-ae (1)