cosmosR
COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.
Science Score: 59.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 3 DOI reference(s) in README -
✓Academic publication links
Links to: biorxiv.org -
✓Committers with academic emails
1 of 11 committers (9.1%) from academic institutions -
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (15.1%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.
Basic Info
- Host: GitHub
- Owner: saezlab
- License: gpl-3.0
- Language: R
- Default Branch: master
- Homepage: https://saezlab.github.io/cosmosR/
- Size: 51.7 MB
Statistics
- Stars: 62
- Watchers: 9
- Forks: 16
- Open Issues: 7
- Releases: 3
Topics
Metadata Files
README.md
cosmosR 
<!-- badges: end -->
Overview
COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets. COSMOS leverages extensive prior knowledge of signaling pathways, metabolic networks, and gene regulation with computational methods to estimate activities of transcription factors and kinases as well as network-level causal reasoning. This pipeline can provide mechanistic explanations for experimental observations across multiple omic data sets.
COSMOS finds coherent subnetwork causally connecting as many deregulated TFs, kinases/phosphatases and metabolites as possible. The subnetwork is extracted from a novel integrated PKN (available here) spanning signaling, transcriptional regulation and metabolism. Transcription factors activities are inferred from gene expression with decoupleR. Kinase activities are inferred from phosphoproteomic with a kinase/substrate network of Omnipath, a meta resource of protein-protein. The scripts to generate the current network can be found here: https://github.com/saezlab/metaPKNBIGG.
You can also use COSMOS if you don't have metabolomic data, to connect TF activities (from transcriptomic) with kinase activities (from phosphoproteomic) for exmaple !
Installation
R >= 4.1 is required ```r
install from bioconductor
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("cosmosR")
We advise to instal from github to get the latest version of the tool.
if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")
devtools::install_github("saezlab/cosmosR") ```
If you don't have R 4.1, you can also clone the github repository on your machine, create a new R project with R studio from the cosmosR folder, change the R version to your own R version in the DESCRIPTION file and then install it with devtools:install()
But 4.1 is advised in any case.
tutorial to use MOFA and COSMOS
Here you can find an extensive tutorial showing how to use MOFA and COSMOS with the NCI60 dataset. This is an extensive tutorial, if you wish to get a quicker plug and play introduction to COSMOS, see below.
!!! THIS is were you can find the input data and the pre-processing scripts that corespond to the featured vignette !!!
Tutorial (NCI60 playground)
We made a repository that contains pre-processed inputs and an example script to use cosmos with the NCI60 RNA+metabolomic datasets. You can find the repository here.
!!! THIS is were you can find the input data and the pre-processing scripts that corespond to the featured vignette !!!
Access
The meta PKN used with the older biorXiv version of COSMOS (2021) is available here.
An updated meta PKN is available with the package (using data(meta_network) in R)
Citation
If you use cosmosR for your research please cite COSMOS+ preprint Dugourd A, Lafrenz P, Mañanes D, Fallegger R, Kroger AC, Turei D, Shtylla B, Saez-Rodriguez J; Modeling causal signal propagation in multi-omic factor space with COSMOS; BioRxiv. 2024 Jul 17 DOI: 10.1101/2024.07.15.603538
The first publication of COSMOS is MSB can be found here:
License
The code is distributed under the GNU General Public License v3.0. The meta PKN is distributed under the Attribution-NonCommercial 4.0 International (CC-BY-NC 4.0) License.
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
- Watch event: 5
- Issue comment event: 2
- Push event: 5
- Fork event: 1
Last Year
- Watch event: 5
- Issue comment event: 2
- Push event: 5
- Fork event: 1
Committers
Last synced: 9 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| adugourd | a****d@u****e | 137 |
| Attila Gabor | g****7@g****m | 126 |
| Katharina Zirngibl | k****l@g****m | 49 |
| Christian | c****8@g****m | 19 |
| Aurelien Dugourd | A****n@A****l | 9 |
| Nitesh Turaga | n****a@g****m | 6 |
| Caroline2501 | c****7@g****e | 5 |
| deeenes | t****s@g****m | 5 |
| Martin Garrido Rodriguez-Cordoba | m****f@g****m | 4 |
| J Wokaty | j****y | 4 |
| Christian Holland | c****d@b****e | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 24
- Total pull requests: 17
- Average time to close issues: 4 months
- Average time to close pull requests: 19 days
- Total issue authors: 18
- Total pull request authors: 6
- Average comments per issue: 3.25
- Average comments per pull request: 0.65
- Merged pull requests: 16
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 6
- Pull requests: 0
- Average time to close issues: about 2 months
- Average time to close pull requests: N/A
- Issue authors: 4
- Pull request authors: 0
- Average comments per issue: 2.5
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- narmadabc (2)
- an-altosian (2)
- SwagatikaSahoo2023 (2)
- adugourd (2)
- CatherM (1)
- Kriti1594 (1)
- jtorrejon81 (1)
- LonnekeNouwen (1)
- samuelbunga (1)
- wmoldham (1)
- jytan01 (1)
- transform66 (1)
- dilipgosar (1)
- anu-bioinfo (1)
- Eirinits (1)
Pull Request Authors
- adugourd (8)
- christianholland (4)
- gabora (2)
- martingarridorc (1)
- clohoff (1)
- deeenes (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 8,982 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: cosmosR
COSMOS (Causal Oriented Search of Multi-Omic Space)
- Homepage: https://github.com/saezlab/COSMOSR
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/cosmosR/inst/doc/cosmosR.pdf
- License: GPL-3
-
Latest release: 1.16.0
published 10 months ago
Rankings
Maintainers (1)
Dependencies
- R >= 4.1 depends
- CARNIVAL * imports
- GSEABase * imports
- dorothea * imports
- dplyr * imports
- igraph * imports
- progress * imports
- purrr * imports
- rlang * imports
- stringr * imports
- utils * imports
- visNetwork * imports
- ggplot2 * suggests
- knitr * suggests
- piano * suggests
- rmarkdown * suggests
- testthat * suggests
- actions/cache v2 composite
- actions/checkout v2 composite
- actions/upload-artifact master composite
- docker/build-push-action v1 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite