Science Score: 36.0%
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○CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
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○DOI references
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✓Academic publication links
Links to: pubmed.ncbi, ncbi.nlm.nih.gov -
○Committers with academic emails
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○Scientific vocabulary similarity
Low similarity (7.1%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
DEqMS is a tool for quantitative proteomic analysis
Basic Info
- Host: GitHub
- Owner: yafeng
- Language: R
- Default Branch: master
- Size: 17 MB
Statistics
- Stars: 23
- Watchers: 4
- Forks: 3
- Open Issues: 14
- Releases: 0
Topics
Metadata Files
README.md
DEqMS
DEqMS is a statistical tool for testing differential protein expression in quantitative proteomic analysis, developed by Yafeng Zhu @ Karolinska Institutet.
DEqMS is a published method, if you use it in your research, please cite: Zhu et al. DEqMS: A Method for Accurate Variance Estimation in Differential Protein Expression Analysis. Mol Cell Proteomics 2020 Mar 23. PMID: 32205417
Installation
To install lastest DEqMS package (v1.6.0), start R (version "4.0") and enter: ```{r}
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("DEqMS")
```
Introduction
DEqMS is developed on top of Limma. However, Limma assumes same prior variance for all genes. In proteomics, the accuracy of protein abundance estimates varies by the number of peptides/PSMs quantified in both label-free and labelled data. Proteins quantification by multiple peptides or PSMs are more accurate. DEqMS package is able to estimate different prior variances for proteins quantified by different number of PSMs/peptides, therefore achieving better accuracy. The package can be applied to analyze both label-free and labelled proteomics data.
How to use it
Browse DEqMS online Vignettes here
Owner
- Login: yafeng
- Kind: user
- Location: Boston
- Company: Harvard medical school
- Repositories: 6
- Profile: https://github.com/yafeng
GitHub Events
Total
- Issues event: 4
- Watch event: 2
- Issue comment event: 13
- Push event: 4
- Pull request event: 3
- Fork event: 1
- Create event: 1
Last Year
- Issues event: 4
- Watch event: 2
- Issue comment event: 13
- Push event: 4
- Pull request event: 3
- Fork event: 1
- Create event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Yafeng Zhu | y****u@s****e | 66 |
| Yafeng Zhu | y****u@y****e | 23 |
| yafeng | y****u@o****m | 17 |
| Jorrit Boekel | j****l@s****e | 4 |
| Nitesh Turaga | n****a@g****m | 4 |
| Yafeng Zhu | y****u@Y****l | 4 |
| vobencha | v****a@g****m | 2 |
| Kayla-Morrell | k****l@r****g | 1 |
| Yafeng Zhu | y****u@Y****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 2
- Total pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 2
- Total pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- 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: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- potockym (1)
- lisiarend (1)
- jesswhitts (1)
- nomascus (1)
- longchung90 (1)
- yudada2020 (1)
- Arthfael (1)
- 14stutzmanav (1)
Pull Request Authors
- yafeng (2)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- R >= 3.5 depends
- ggplot2 * depends
- graphics * depends
- limma >= 3.34 depends
- stats * depends
- BiocStyle * suggests
- ExperimentHub * suggests
- LSD * suggests
- farms * suggests
- ggrepel * suggests
- knitr * suggests
- matrixStats * suggests
- plyr * suggests
- reshape2 * suggests
- rmarkdown * suggests
- utils * suggests