einprot
einprot: flexible, easy-to-use, reproducible workflows for statistical analysis of quantitative proteomics data - Published in JOSS (2023)
Science Score: 93.0%
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Published in Journal of Open Source Software
Repository
Proteomics analysis workflows
Basic Info
- Host: GitHub
- Owner: fmicompbio
- License: other
- Language: R
- Default Branch: main
- Homepage: https://fmicompbio.github.io/einprot/
- Size: 25.2 MB
Statistics
- Stars: 7
- Watchers: 3
- Forks: 1
- Open Issues: 3
- Releases: 5
Metadata Files
README.md
einprot
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The einprot package contains a set of workflows for statistical analysis
of quantitative proteomics data processed with MaxQuant (LFQ), FragPipe (LFQ)
or Proteome Discoverer (TMT-labelled).
Installation
You can install the development version of einprot from
GitHub, e.g. using
BiocManager:
r
install.packages("BiocManager")
BiocManager::install("fmicompbio/einprot")
Usage
For more details about how to use einprot, we refer to the
vignette.
A collection of example reports generated by applying einprot to a variety of
public data sets is available here.
Citation
If you are using einprot, please cite
Soneson C, Iesmantavicius V, Hess D, Stadler MB, Seebacher J (2023). einprot: flexible, easy-to-use, reproducible workflows for statistical analysis of quantitative proteomics data. Journal of Open Source Software, 8(89), 5750.
Need help?
If you run into problems when using einprot, please first check whether the
answer is available in the help pages for the individual functions or in
the vignette.
If not, please open an issue
and explain your problem. Try to provide a reproducible example, and always
include the code you used, that will make it much easier for us to help.
Contributions
If you would like to contribute to einprot, you can do so by sending a pull
request to this repository. If the contribution involves changes in the
functionality provided by einprot, we encourage you to first open an issue
to discuss the intended contribution.
Owner
- Login: fmicompbio
- Kind: user
- Repositories: 17
- Profile: https://github.com/fmicompbio
JOSS Publication
einprot: flexible, easy-to-use, reproducible workflows for statistical analysis of quantitative proteomics data
Authors
Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland, SIB Swiss Institute of Bioinformatics, Basel, Switzerland
Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland, SIB Swiss Institute of Bioinformatics, Basel, Switzerland, University of Basel, Switzerland
Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
Editor
Frederick Boehm
Tags
proteomicsGitHub Events
Total
- Issues event: 2
- Watch event: 1
- Delete event: 1
- Issue comment event: 1
- Push event: 17
- Pull request event: 2
- Fork event: 1
Last Year
- Issues event: 2
- Watch event: 1
- Delete event: 1
- Issue comment event: 1
- Push event: 17
- Pull request event: 2
- Fork event: 1
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Charlotte Soneson | c****n@g****m | 887 |
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 13
- Total pull requests: 12
- Average time to close issues: about 1 month
- Average time to close pull requests: about 15 hours
- Total issue authors: 6
- Total pull request authors: 1
- Average comments per issue: 4.92
- Average comments per pull request: 0.42
- Merged pull requests: 12
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 3
- Pull requests: 0
- Average time to close issues: 12 days
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 1.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- skiaphrene (6)
- tobiasko (3)
- vcoyne1 (1)
- liorlobel (1)
- AnthonyOfSeattle (1)
- ByrumLab (1)
Pull Request Authors
- csoneson (15)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- R >= 4.0 depends
- BiocSingular * imports
- ComplexHeatmap * imports
- ComplexUpset * imports
- DT * imports
- ExploreModelMatrix * imports
- GSEABase * imports
- IRanges * imports
- MsCoreUtils * imports
- QFeatures * imports
- S4Vectors * imports
- STRINGdb * imports
- SingleCellExperiment * imports
- SummarizedExperiment * imports
- XML * imports
- babelgene * imports
- circlize * imports
- cowplot * imports
- dplyr * imports
- genefilter * imports
- ggiraph * imports
- ggplot2 * imports
- ggrepel * imports
- grDevices * imports
- htmltools * imports
- iSEE * imports
- iSEEu * imports
- imputeLCMD * imports
- kableExtra * imports
- knitr * imports
- limma * imports
- mclust * imports
- methods * imports
- msigdbr * imports
- plotly * imports
- readr * imports
- rlang * imports
- rmarkdown * imports
- rrcovNA * imports
- scales * imports
- scater * imports
- stats * imports
- stringr * imports
- tibble * imports
- tidyr * imports
- utils * imports
- vsn * imports
- xfun * imports
- xml2 * imports
- BiocManager * suggests
- testthat >= 3.0.0 suggests
- actions/cache v1 composite
- actions/checkout v2 composite
- actions/upload-artifact master composite
- grimbough/bioc-actions/build-install-check v1 composite
- grimbough/bioc-actions/setup-bioc v1 composite
- r-lib/actions/setup-pandoc master composite