OmniPath @omnipathdb
OmniPath: molecular biology knowledge from 100+ databases omnipathdb.org Heidelberg, Germany Joined October 2017-
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Building a knowledge graph for biomedical tasks usually takes months or years. 😰 What if you could do it in weeks or days? 🏃 We created BioCypher (biocypher.org) to make it easier than ever, but still flexible and transparent. 🧵⬇️
Check out LIANA that uses @omnipathdb to systematically compare and combine resources & methods to study cell-cell communication from #scRNA
Check out LIANA that uses @omnipathdb to systematically compare and combine resources & methods to study cell-cell communication from #scRNA
We have also added several tutorials showing how to use decoupler and @omnipathdb in single cell analyses such as automatic cell type annotation, transcription factor and pathway activity inference. Documentation and tutorials available in: decoupler-py.readthedocs.io
We are looking for PostDosc/ PhDs in Medical Bioinformatics & Machine Learning @uniklinik_hd @UniHeidelberg #multiomics #singlecell consider applying and pls RT 🙏 jobrxiv.org/job/heidelberg…
Check MISTy from @tanevski et al @saezlab to analyze spatial omics - they used @omnipathdb 's annotated prior knowledge to link intracellular pathway activities & the expression of ligands in space 👇
Check MISTy from @tanevski et al @saezlab to analyze spatial omics - they used @omnipathdb 's annotated prior knowledge to link intracellular pathway activities & the expression of ligands in space 👇
Our updated manuscript describing methods for bioactivity inference (pathways, TFs, etc.) is now published in @BioinfoAdv doi.org/10.1093/bioadv… 🥳 We have been working on a new #Python 🐍 implementation and its integration with the meta-resource @omnipathdb 👇
Our updated manuscript describing methods for bioactivity inference (pathways, TFs, etc.) is now published in @BioinfoAdv doi.org/10.1093/bioadv… 🥳 We have been working on a new #Python 🐍 implementation and its integration with the meta-resource @omnipathdb 👇
The great spatial omics platform from @fabian_theis group is out in @naturemethods 🥳 Squidpy uses OmniPath data for ligand-receptor interactions 🤩 Special thanks to Michal Klein for implementing the OmniPath Python client✌️
The great spatial omics platform from @fabian_theis group is out in @naturemethods 🥳 Squidpy uses OmniPath data for ligand-receptor interactions 🤩 Special thanks to Michal Klein for implementing the OmniPath Python client✌️
Our paper is among the 8 most read in @MolSystBiol embopress.org/doi/full/10.15…, and got already 27 citations! 🎉 In @saezlab & @KorcsmarosLab it's a great pleasure for us to see you using our work. Meanwhile we are preparing big new developments, stay tuned 😉
Check out #COVID19 Disease Map Consortia @CovidPathways knowledge repository embopress.org/doi/full/10.15…, great community effort where we contributed @omnipathdb (pathway knowledge), DOROTHEA saezlab.github.io/dorothea (TF targets) & CARNIVAL saezlab.github.io/CARNIVAL (network modeling)
We just talked about OmnipathR at BioC2021 @Bioconductor, many thanks to all the participants and the organizers! 🌞 Slides: static.omnipathdb.org/bioc-omnipath_… Vignette (and further materials): saezlab.github.io/OmnipathR/arti… Other @saezlab tools: saezlab.org/#tools
11 #PPI scores based on structure, sequence and function from PrePPI of Honig Lab @Columbia 🌴honiglab.c2b2.columbia.edu/PrePPI 🌴 Now easy access with our R package: static.omnipathdb.org/omnipathr_manu… 🌴 github.com/saezlab/Omnipa…
6,225 new protein complexes in OmniPath thanks to hu.MAP 2.0 from @kdrew @jbwallingford & @edward_marcotte 🖥️ omnipathdb.org/complexes?reso…, 🏡 humap2.proteincomplexes.org, 📰 embopress.org/doi/full/10.15…
Human Cell Map from @gingraslab1 is available in OmniPath! ⭐️ Subcellular localization of 6,000+ proteins from a BioID screen in HEK cells: cell-map.org, nature.com/articles/s4158…
Estimate ligand activities from #transcriptomics with the new OmniPath-NicheNet workflow 🤩 workflows.omnipathdb.org/#nichenet 🤩 Customizable networks from OmniPath & other resources + NicheNet algorithm from @RobinBrowaeys of @saeyslab
Check out my first first-author work with @ManishButte! We used @omnipathdb, a protein interactions meta-database, as well as RNAseq data from @ProteinAtlas to expand the potential genes of inborn errors of immunity (IEIs). Hoping immunology clinics worldwide will find it useful!
Check out my first first-author work with @ManishButte! We used @omnipathdb, a protein interactions meta-database, as well as RNAseq data from @ProteinAtlas to expand the potential genes of inborn errors of immunity (IEIs). Hoping immunology clinics worldwide will find it useful!
Happy that @omnipathdb was helpful as a meta-resource of cell-cell interaction resources in this comparison of methods to estimate cell-cell communication from scRNA-seq data
Happy that @omnipathdb was helpful as a meta-resource of cell-cell interaction resources in this comparison of methods to estimate cell-cell communication from scRNA-seq data
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