resources.yaml

order:
- BioCypher
- CARNIVAL
- CellNOpt
- CollecTRI
- CORNETO
- COSMOS
- Decoupler
- DoRothEA
- DOT
- LIANA+
- MetalinksDB
- MetaProViz
- MISTy
- NetworkCommons
- ocEAn
- OmniPath
- PHONEMeS
- PROGENy
resources:
  BioCypher:
    main: A unifying framework for biomedical research knowledge graphs
    links:
    - - home
      - https://biocypher.org/
    - - python
      - https://github.com/saezlab/BioCypher
    - - package:PYPI
      - https://pypi.org/project/biocypher/
    - - article
      - https://zenodo.org/records/10320714
  CARNIVAL:
    main: Causal reasoning to explore mechanisms in molecular networks
    links:
    - - home
      - https://saezlab.github.io/CARNIVAL
    - - r
      - https://github.com/saezlab/CARNIVAL
    - - package:BIOC
      - https://bioconductor.org/packages/release/bioc/html/CARNIVAL.html
    - - article
      - https://europepmc.org/abstract/MED/31728204
  CellNOpt:
    main: Train logic models of signaling against omics data
    links:
    - - home
      - https://saezlab.github.io/CellNOptR/
    - - r
      - https://github.com/saezlab/cellnopt
    - - package:BIOC
      - https://bioconductor.org/packages/release/bioc/html/CellNOptR.html
    - - python
      - https://github.com/cellnopt/cellnopt
    - - article
      - https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa561/5855133
  CollecTRI:
    main: Collection of Transcriptional Regulatory Interactions
    links:
    - - main
      - https://github.com/saezlab/CollecTRI
    - - r
      - https://github.com/saezlab/CollecTRI
    - - article
      - http://europepmc.org/abstract/MED/37843125
    - - r
      - https://r.omnipathdb.org/reference/collectri.html
    - - python
      - https://github.com/saezlab/omnipath/blob/ab2e17189bbafa2f20621e4890c3da02d4ba6c76/omnipath/_core/requests/interactions/_interactions.py#L237
  CORNETO:
    main: Unified framework for network inference problems
    links:
    - - python
      - https://github.com/saezlab/corneto
    - - package:PYPI
      - https://pypi.org/project/corneto/
    - - article
      - https://www.biorxiv.org/content/10.1101/2024.10.26.620390v1
  COSMOS:
    main: Mechanistic insights across multiple omics
    links:
    - - home
      - https://saezlab.github.io/cosmosR/
    - - r
      - https://github.com/saezlab/COSMOS/
    - - package:BIOC
      - https://bioconductor.org/packages/release/bioc/html/cosmosR.html
    - - python
      - https://networkcommons.readthedocs.io/en/main/api/networkcommons.data.network.get_cosmos_pkn.html#networkcommons.data.network.get_cosmos_pkn
    - - r
      - https://r.omnipathdb.org/articles/cosmos.html
    - - article
      - https://europepmc.org/abstract/MED/33502086
    - - article
      - https://www.biorxiv.org/content/10.1101/2024.07.15.603538v2
  Decoupler:
    main: Infer biological activities from omics data using a collection of methods
    links:
    - - home
      - https://decoupler-py.readthedocs.io/en/latest/index.html
    - - python
      - https://github.com/saezlab/decoupler-py
    - - package:PYPI
      - https://pypi.org/project/decoupler/
    - - r
      - https://github.com/saezlab/decoupleR
    - - package:BIOC
      - https://bioconductor.org/packages/release/bioc/html/decoupleR.html
    - - article
      - https://academic.oup.com/bioinformaticsadvances/article/2/1/vbac016/6544613?login=false
  DoRothEA:
    main: Transcription factor activity inference
    links:
    - - main
      - https://decoupler-py.readthedocs.io/en/latest/notebooks/dorothea.html
    - - python
      - https://github.com/saezlab/decoupler-py
    - - docs-py
      - https://decoupler-py.readthedocs.io/en/latest/notebooks/dorothea.html
    - - r
      - https://github.com/saezlab/dorothea
    - - r
      - https://r.omnipathdb.org/reference/omnipath-interactions.html
    - - article
      - https://europepmc.org/abstract/MED/31340985
    - - article
      - https://europepmc.org/abstract/MED/29229604
    - - article
      - https://europepmc.org/abstract/MED/31525460
  DOT:
    main: Optimization framework for transferring cell features from a reference data
      to spatial omics
    links:
    - - home
      - https://saezlab.github.io/DOT/
    - - r
      - https://github.com/saezlab/DOT/
    - - article
      - https://arxiv.org/abs/2301.01682
  LIANA+:
    main: Framework to infer inter- and intra-cellular signalling from single-cell
      and spatial omics
    links:
    - - home
      - https://liana-py.readthedocs.io/
    - - home
      - https://saezlab.github.io/liana/
    - - python
      - https://github.com/saezlab/liana-py
    - - r
      - https://github.com/saezlab/liana
    - - article
      - https://www.biorxiv.org/content/10.1101/2023.08.19.553863v1
    - - article
      - https://www.nature.com/articles/s41467-022-30755-0
  MetalinksDB:
    main: Database of protein-metabolite and small molecule ligand-receptor interactions
    links:
    - - home
      - https://metalinks.omnipathdb.org/
    - - python
      - https://github.com/saezlab/MetalinksDB/
    - - article
      - https://academic.oup.com/bib/article/25/4/bbae347/7717953
  MetaProViz:
    main: Metabolomics functional analysis and visualization
    links:
    - - home
      - https://saezlab.github.io/MetaProViz/
    - - r
      - https://github.com/saezlab/MetaProViz
  MISTy:
    main: Explainable machine learning models for single-cell, highly
      multiplexed, spatially resolved data
    links:
    - - home
      - https://saezlab.github.io/mistyR/
    - - r
      - https://github.com/saezlab/mistyR/
    - - package:BIOC
      - https://bioconductor.org/packages/release/bioc/html/mistyR.html
    - - article
      - https://doi.org/10.1186/s13059-022-02663-5
  NetworkCommons:
    main: Context specific networks from omics data and prior-knowledge
    links:
    - - home
      - https://networkcommons.readthedocs.io/
    - - python
      - https://github.com/saezlab/networkCommons
    - - package:PYPI
      - https://pypi.org/project/networkcommons/
    - - article
      - https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaf048/8002097
  ocEAn:
    main: Metabolic enzyme enrichment analysis
    links:
    - - home
      - https://saezlab.github.io/ocean/
    - - r
      - https://github.com/saezlab/ocean
    - - article
      - http://europepmc.org/article/MED/36539415
  OmniPath:
    main: Networks, pathways, gene annotations from 180+ databases
    links:
    - - home
      - https://omnipathdb.org/
    - - r
      - https://github.com/saezlab/OmnipathR
    - - docs-r
      - https://r.omnipathdb.org/
    - - package:BIOC
      - https://bioconductor.org/packages/release/bioc/html/OmnipathR.html
    - - python
      - https://github.com/saezlab/omnipath
    - - docs-py
      - https://omnipath.readthedocs.io/
    - - package:PYPI
      - https://pypi.org/project/omnipath/
    - - python
      - https://github.com/saezlab/pypath
    - - docs-py
      - https://pypath.omnipathdb.org/
    - - package:PYPI
      - https://pypi.org/project/pypath-omnipath/
    - - cytoscape
      - https://github.com/saezlab/Omnipath_Cytoscape
    - - package:CYTO
      - https://apps.cytoscape.org/apps/omnipath
    - - article
      - https://www.embopress.org/doi/epdf/10.15252/msb.20209923
    - - article
      - https://rdcu.be/m53B
    - - article
      - https://www.ncbi.nlm.nih.gov/pubmed/31886476
  PHONEMeS:
    main: Logic modeling of phosphoproteomics
    links:
    - - home
      - https://saezlab.github.io/PHONEMeS/
    - - r
      - https://github.com/saezlab/PHONEMeS
    - - r
      - https://github.com/saezlab/PHONEMeS-ILP
    - - article
      - https://pubs.acs.org/doi/10.1021/acs.jproteome.0c00958
    - - article
      - https://europepmc.org/abstract/MED/26354681
  PROGENy:
    main: Activities of canonical pathways from transcriptomics data
    links:
    - - home
      - https://saezlab.github.io/progeny/
    - - r
      - https://github.com/saezlab/progeny
    - - python
      - https://github.com/saezlab/decoupler-py
    - - package:BIOC
      - https://bioconductor.org/packages/release/bioc/html/progeny.html
    - - article
      - https://europepmc.org/abstract/MED/29295995
    - - article
      - https://europepmc.org/abstract/MED/31525460