137 related articles for article (PubMed ID: 34570431)
1. NDEx: Accessing Network Models and Streamlining Network Biology Workflows.
Pillich RT; Chen J; Churas C; Liu S; Ono K; Otasek D; Pratt D
Curr Protoc; 2021 Sep; 1(9):e258. PubMed ID: 34570431
[TBL] [Abstract][Full Text] [Related]
2. NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange.
Pillich RT; Chen J; Churas C; Fong D; Gyori BM; Ideker T; Karis K; Liu SN; Ono K; Pico A; Pratt D
Bioinformatics; 2023 Mar; 39(3):. PubMed ID: 36882166
[TBL] [Abstract][Full Text] [Related]
3. NDEx: A Community Resource for Sharing and Publishing of Biological Networks.
Pillich RT; Chen J; Rynkov V; Welker D; Pratt D
Methods Mol Biol; 2017; 1558():271-301. PubMed ID: 28150243
[TBL] [Abstract][Full Text] [Related]
4. CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API.
Ono K; Muetze T; Kolishovski G; Shannon P; Demchak B
F1000Res; 2015; 4():478. PubMed ID: 26672762
[TBL] [Abstract][Full Text] [Related]
5. Using EMBL-EBI Services via Web Interface and Programmatically via Web Services.
Madeira F; Madhusoodanan N; Lee J; Eusebi A; Niewielska A; Tivey ARN; Meacham S; Lopez R; Butcher S
Curr Protoc; 2024 Jun; 4(6):e1065. PubMed ID: 38857087
[TBL] [Abstract][Full Text] [Related]
6. NDEx, the Network Data Exchange.
Pratt D; Chen J; Welker D; Rivas R; Pillich R; Rynkov V; Ono K; Miello C; Hicks L; Szalma S; Stojmirovic A; Dobrin R; Braxenthaler M; Kuentzer J; Demchak B; Ideker T
Cell Syst; 2015 Oct; 1(4):302-305. PubMed ID: 26594663
[TBL] [Abstract][Full Text] [Related]
7. Data-dependent visualization of biological networks in the web-browser with NDExEdit.
Auer F; Mayer S; Kramer F
PLoS Comput Biol; 2022 Jun; 18(6):e1010205. PubMed ID: 35675360
[TBL] [Abstract][Full Text] [Related]
8. Cytoscape Automation: empowering workflow-based network analysis.
Otasek D; Morris JH; Bouças J; Pico AR; Demchak B
Genome Biol; 2019 Sep; 20(1):185. PubMed ID: 31477170
[TBL] [Abstract][Full Text] [Related]
9. NDEx 2.0: A Clearinghouse for Research on Cancer Pathways.
Pratt D; Chen J; Pillich R; Rynkov V; Gary A; Demchak B; Ideker T
Cancer Res; 2017 Nov; 77(21):e58-e61. PubMed ID: 29092941
[TBL] [Abstract][Full Text] [Related]
10. RCy3: Network biology using Cytoscape from within R.
Gustavsen JA; Pai S; Isserlin R; Demchak B; Pico AR
F1000Res; 2019; 8():1774. PubMed ID: 31819800
[TBL] [Abstract][Full Text] [Related]
11. Automated exploration of gene ontology term and pathway networks with ClueGO-REST.
Mlecnik B; Galon J; Bindea G
Bioinformatics; 2019 Oct; 35(19):3864-3866. PubMed ID: 30847467
[TBL] [Abstract][Full Text] [Related]
12. CyTargetLinker app update: A flexible solution for network extension in Cytoscape.
Kutmon M; Ehrhart F; Willighagen EL; Evelo CT; Coort SL
F1000Res; 2018; 7():. PubMed ID: 31489175
[TBL] [Abstract][Full Text] [Related]
13. ndexr-an R package to interface with the network data exchange.
Auer F; Hammoud Z; Ishkin A; Pratt D; Ideker T; Kramer F
Bioinformatics; 2018 Feb; 34(4):716-717. PubMed ID: 29087446
[TBL] [Abstract][Full Text] [Related]
14. Workflows for microarray data processing in the Kepler environment.
Stropp T; McPhillips T; Ludäscher B; Bieda M
BMC Bioinformatics; 2012 May; 13():102. PubMed ID: 22594911
[TBL] [Abstract][Full Text] [Related]
15. Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data.
Doncheva NT; Morris JH; Gorodkin J; Jensen LJ
J Proteome Res; 2019 Feb; 18(2):623-632. PubMed ID: 30450911
[TBL] [Abstract][Full Text] [Related]
16. Biowep: a workflow enactment portal for bioinformatics applications.
Romano P; Bartocci E; Bertolini G; De Paoli F; Marra D; Mauri G; Merelli E; Milanesi L
BMC Bioinformatics; 2007 Mar; 8 Suppl 1(Suppl 1):S19. PubMed ID: 17430563
[TBL] [Abstract][Full Text] [Related]
17. scNetViz: from single cells to networks using Cytoscape.
Choudhary K; Meng EC; Diaz-Mejia JJ; Bader GD; Pico AR; Morris JH
F1000Res; 2021; 10():. PubMed ID: 34912541
[TBL] [Abstract][Full Text] [Related]
18. CytoITMprobe: a network information flow plugin for Cytoscape.
Stojmirović A; Bliskovsky A; Yu YK
BMC Res Notes; 2012 May; 5():237. PubMed ID: 22587372
[TBL] [Abstract][Full Text] [Related]
19. aMatReader: Importing adjacency matrices via Cytoscape Automation.
Settle B; Otasek D; Morris JH; Demchak B
F1000Res; 2018; 7():. PubMed ID: 30026937
[TBL] [Abstract][Full Text] [Related]
20. Harnessing the 3D-Beacons Network: A Comprehensive Guide to Accessing and Displaying Protein Structure Data.
Magaña P; Nair S; Varadi M; Velankar S
Curr Protoc; 2024 May; 4(5):e1047. PubMed ID: 38720559
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]