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
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○.zenodo.json file
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✓DOI references
Found 9 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
5 of 15 committers (33.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (11.2%) to scientific vocabulary
Keywords from Contributors
Repository
R package for Pathway RespOnsive GENe activity inference
Basic Info
- Host: GitHub
- Owner: saezlab
- License: apache-2.0
- Language: R
- Default Branch: master
- Homepage: https://saezlab.github.io/progeny/
- Size: 47.9 MB
Statistics
- Stars: 108
- Watchers: 17
- Forks: 21
- Open Issues: 3
- Releases: 0
Metadata Files
README.md
PROGENy: Pathway RespOnsive GENes for activity inference 
Overview
PROGENy is resource that leverages a large compendium of publicly available signaling perturbation experiments to yield a common core of pathway responsive genes for human and mouse. These, coupled with any statistical method, can be used to infer pathway activities from bulk or single-cell transcriptomics.
This is an R package for storing the pathway signatures. To infer pathway activities, please check out decoupleR, available in R or python.
Installation
Progeny is available in Bioconductor. In addition, one can install the development version from the Github repository:
```r
To install the package from Bioconductor
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("progeny")
To install the development version from the Github repo:
devtools::install_github("saezlab/progeny") ```
Updates
Since the original release, we have implemented some extensions in PROGENy:
- Extension to mouse: Originally PROGENy was developed for the application to human data. In a benchmark study we showed that PROGENy is also applicable to mouse data, as described in Holland et al., 2019. Accordingly, we included new parameters to run mouse version of PROGENy by transforming the human genes to their mouse orthologs.
- Expanding Pathway Collection: We expanded human and mouse PROGENy with the pathways Androgen, Estrogen and WNT.
- Extension to single-cell RNA-seq data: We showed that PROGENy can be applied to scRNA-seq data, as described in Holland et al., 2020
Citation
Schubert M, Klinger B, Klünemann M, Sieber A, Uhlitz F, Sauer S, Garnett MJ, Blüthgen N, Saez-Rodriguez J. 2018. Perturbation-response genes reveal signaling footprints in cancer gene expression. Nature Communications: 10.1038/s41467-017-02391-6
Owner
- Name: Saez Lab
- Login: saezlab
- Kind: organization
- Email: pub.saez@uni-heidelberg.de
- Location: Germany
- Website: saezlab.org
- Repositories: 241
- Profile: https://github.com/saezlab
Institute for Computational Biomedicine - Julio Saez-Rodriguez's group
GitHub Events
Total
- Issues event: 3
- Watch event: 14
- Issue comment event: 3
- Fork event: 3
Last Year
- Issues event: 3
- Watch event: 14
- Issue comment event: 3
- Fork event: 3
Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Igor Bulanov | b****g@p****u | 130 |
| mschubert | m****v@g****m | 37 |
| Alberto Valdeolivas | a****s@g****m | 36 |
| adugourd | a****d@b****e | 15 |
| Nitesh Turaga | n****a@g****m | 12 |
| PauBadiaM | p****a@u****e | 9 |
| deeenes | t****s@g****m | 5 |
| Christian Holland | c****8@g****m | 4 |
| vobencha | v****a@g****m | 2 |
| Igor Bulanov | 3****v | 2 |
| Hervé Pagès | h****s@f****g | 2 |
| vobencha | v****n@r****g | 2 |
| Julio Saez-Rodriguez | j****z@u****e | 1 |
| Jan Gleixner | j****r@g****m | 1 |
| Federico Marini | m****f@u****e | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 53
- Total pull requests: 11
- Average time to close issues: 10 months
- Average time to close pull requests: about 1 month
- Total issue authors: 40
- Total pull request authors: 7
- Average comments per issue: 1.66
- Average comments per pull request: 0.64
- Merged pull requests: 11
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 7
- Pull requests: 0
- Average time to close issues: 14 days
- Average time to close pull requests: N/A
- Issue authors: 7
- 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
- mschubert (6)
- yesitsjess (3)
- enblacar (3)
- HocheolJang426 (2)
- messersc (2)
- Caary (2)
- christianholland (2)
- blinggi (1)
- AndreaGuarracino (1)
- asumann (1)
- shengqh (1)
- jperales (1)
- Vernonjustice (1)
- Tommaso12 (1)
- CB-postech (1)
Pull Request Authors
- PauBadiaM (3)
- christianholland (2)
- deeenes (2)
- adugourd (1)
- jan-glx (1)
- federicomarini (1)
- alberto-valdeolivas (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 41,765 total
- Total dependent packages: 2
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: progeny
Pathway RespOnsive GENes for activity inference from gene expression
- Homepage: https://github.com/saezlab/progeny
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/progeny/inst/doc/progeny.pdf
- License: Apache License (== 2.0) | file LICENSE
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Latest release: 1.30.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.6.0 depends
- Biobase * imports
- decoupleR * imports
- dplyr * imports
- ggplot2 * imports
- ggrepel * imports
- gridExtra * imports
- reshape2 * imports
- stats * imports
- tidyr * imports
- BiocFileCache * suggests
- BiocStyle * suggests
- DESeq2 * suggests
- Seurat * suggests
- SingleCellExperiment * suggests
- airway * suggests
- biomaRt * suggests
- broom * suggests
- knitr * suggests
- pheatmap * suggests
- readr * suggests
- readxl * suggests
- rmarkdown * suggests
- testthat >= 2.1.0 suggests
- tibble * suggests