Cytoscape Software Authors: Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T Cited in: 43 Publications (2007–2022) Related Software: KEGG; R; IntAct; Bioconductor; Gephi; BioGRID; … Main Fields: –
RegulonDB Software Authors: Gama-Castro, S.; Jimenez-Jacinto, V.; Peralta-Gil, M.; Santos-Zavaleta, A.; Peñaloza-Spinola, M.I.; Contreras-Moreira, B.; Segura-Salazar, J.; Muñiz-Rascado, L.; Martinez-Flores, I.; Salgado, H.; Bonavides-Martinez, C.; Abreu-Goodger, C.; Rodríguez-Penagos, C.; Miranda-Ríos, J.; Morett, E.; Merino, E.; Huerta, A.M.; Treviño-Quintanilla, L.; Collado-Vides, J. Cited in: 30 Publications (2002–2020) Related Software: KEGG; ARACNE; GeneNetWeaver; R; WebLogo; JASPAR; … Main Fields: –
ARACNE Software Authors: A. A. Margolin, I. Nemenman, K. Basso, C. Wiggins, G. Stolovitzky, R. D. Favera, A. Califano Cited in: 34 Publications (2009–2022) Related Software: minet; KEGG; glasso; SynTReN; GeneNetWeaver; R; … Main Fields: –
Ginsim Software Authors: Gonzales, A. G.; Naldi, A.; Sanchez, L.; Thieffry, D.; Chaouiya, C Cited in: 34 Publications (2008–2022) Related Software: BoolNet; GitHub; Macaulay2; ADAM; PyBoolNet; Aeon; … Main Fields: –
REVEAL Software Authors: Liang, S., Fuhrman, S., Somogyi, R Cited in: 22 Publications (2003–2022) Related Software: KEGG; R; BoolNet; E-CELL; GEPASI; Macaulay2; … Main Fields: –
GNA Software Authors: Hidde de Jong, Johannes Geiselmann, Céline Hernandez, Michel Page Cited in: 25 Publications (2006–2021) Related Software: BIOCHAM; KEGG; Celldesigner; RoVerGeNe; DiVinE; Ginsim; … Main Fields: –
SynTReN Software Authors: Van den Bulcke, T., Van Leemput, K., Naudts, B., van Remortel, P., Ma, H., Verschoren, A., De Moor, B.: Marchal, K. Cited in: 14 Publications (2009–2021) Related Software: ARACNE; glasso; R; minet; igraph; GeneNetWeaver; … Main Fields: –
Siconos Software Authors: Siconos development team Cited in: 13 Publications (2010–2022) Related Software: PATH Solver; pvlib; CasADi; Ipopt; ZQPCVX; Meschach; … Main Fields: –
TIGRESS Software Authors: Haury, A.C., Mordelet, F., Vera-Licona, P., Vert, J.P. Cited in: 9 Publications (2013–2019) Related Software: SIRENE; ARACNE; glasso; JASPAR; BioGRID; glmnet; … Main Fields: –
NETWORKINFERENCE Software Authors: Smith, V.Anne; Jarvis, Erich D.; Hartemink, Alexander J. Cited in: 8 Publications (2002–2020) Related Software: Brain Connectivity Toolbox; KEGG; Church; Figaro; PRISM; pcalg; … Main Fields: –
SGN Sim Software Authors: Ribeiro AS, Lloyd-Price J Cited in: 7 Publications (2009–2019) Related Software: RegulonDB; NOMAD; GeneNetWeaver; Path2Models; SOSlib; LASSIE; … Main Fields: –
COXPRESdb Software Authors: Obayashi, T.; Hayashi, S.; Shibaoka, M.; Saeki, M.; Ohta, H.; Kinoshita, K. Cited in: 3 Publications (2011–2022) Related Software: KEGG; ArrayExpress; Cytoscape; Symmetric NMTF; QPLIB; STRING; … Main Fields: –
SIRENE Software Authors: F. Mordelet, J.-P. Vert Cited in: 6 Publications (2013–2019) Related Software: ARACNE; KEGG; R; TIGRESS; UniProt; BioGRID; … Main Fields: –
ConsensusPathDB Software Authors: Kamburov A, Pentchev K, Galicka H et al Cited in: 4 Publications (2011–2018) Related Software: IntAct; BioGRID; igraph; SQUAD; ClueGO; gcrma; … Main Fields: –
NARROMI Software Authors: Zhang, X.; Liu, K.; Liu, Z. P.; Duval, B.; Richer, J. M.; Zhao, X. M.; Hao, J. K.; Chen, L. Cited in: 6 Publications (2014–2019) Related Software: BENEDICT; TETRAD; pcalg; impute; NOMAD; GeneNetWeaver; … Main Fields: –
SPINE Software Authors: Ourfali O, Shlomi T, Ideker T, Ruppin E, Sharan R Cited in: 5 Publications (2012–2022) Related Software: ProbLog; BioGRID; KEGG; R; SMAC; MiniZinc; … Main Fields: –
C-ImmSim Software Authors: Santoni, D.; Pedicini, M.; Castiglione, F. Cited in: 4 Publications (2008–2019) Related Software: SQUAD Main Fields: –
DREAM4 Software Authors: Greenfield, A., A. Madar, H. Ostrer, R. Bonneau Cited in: 4 Publications (2015–2020) Related Software: graphite; TRANSFAC; Biopython; WGCNA; pcalg; GeneNetWeaver; … Main Fields: –
gNCA Software Authors: Linh M. Tran; Mark P. Brynildsen; Katy C. Kao; Jason K. Suen; James C. Lia Cited in: 4 Publications (2009–2010) Related Software: MatInspector; PMA; BRENDA; WinBEST-KIT; ESSYNS; KEGG; … Main Fields: –
KELLER Software Authors: Song L, Kolar M, Xing EP Cited in: 3 Publications (2016–2020) Related Software: glasso; loggle; igraph; R; KEGG; TETRAD; … Main Fields: –
ARACNe-AP Software Authors: Lachmann A, Giorgi FM, Lopez G, Califano A. Cited in: 2 Publications (2018–2019) Related Software: pycit; infotheory; IDTxl; MDEntropy; SciPy; NumPy; … Main Fields: Biology and other natural sciences (92-XX)
ASIAN Software Authors: Aburatani, S.; Goto, K.; Saito, S.; Toh, H.; Horimoto, K. Cited in: 1 Publication (2006) Related Software: MIM Main Fields: –
GeNGe Software Authors: Hache H, Wierling C, Lehrach H, Herwig R Cited in: 1 Publication (2019) Related Software: ARACNE; DINGO; glasso; SynTReN; GeneNetWeaver; RegulonDB; … Main Fields: –
GlobalMIT Software Authors: Vinh, N.X., Chetty, M., Coppel, R., Wangikar, P.P. Cited in: 3 Publications (2015–2021) Related Software: ARACNE; KEGG; slingshot; SNN-Cliq; MrTADFinder; CIDR; … Main Fields: –
HPAM Software Authors: Cotik, V.; Romero Zaliz, R.; Zwir, I. Cited in: 3 Publications (2005–2011) Related Software: RegulonDB; EnsemblePail; GPCR-CA; BacPP; Quat-2L; GPCR-GIA; … Main Fields: (92C40-XX); (92D10-XX); (90C29-XX)
NIMEFI Software Authors: Ruyssinck, J., Huynh-Thu, V.A., Geurts, P., Dhaene, T., Demeester, P., Saeys, Y. Cited in: 2 Publications (2017–2020) Related Software: Espresso; InterpretML; Alibi Explain; auto-sklearn; dalex; AI Explainability 360; … Main Fields: –
OKVAR-Boost Software Authors: Lim N, Senbabaoglu Y, Michailidis G, d'Alché-Buc F. Cited in: 3 Publications (2013–2016) Related Software: ARACNE; fda (R); GeneNetWeaver; G1DBN; UNLocBoX; SIRENE; … Main Fields: –
SCENIC Software Authors: Aibar S, González-Blas CB, Moerman T, Huynh-Thu VA, Imrichova H, Hulselmans G, Rambow F, Marine JC, Geurts P, Aerts J, van den Oord J, Atak ZK, Wouters J, Aerts S Cited in: 3 Publications (2019–2021) Related Software: SCODE; glasso; DINGO; ARACNE; KEGG; WGCNA; … Main Fields: –
bc3net Software Authors: Ricardo de Matos Simoes, Frank Emmert-Streib Cited in: 1 Publication (2017) Related Software: Diffcorr; igraph; R; VCNet; edgeR; ARACNE; … Main Fields: Biology and other natural sciences (92-XX)
BioTapestry Software Authors: Institute for Systems Biology (ISB); William Longabaugh; Eric Davidson; Hamid Bolouri; et al. Cited in: 2 Publications (2011–2020) Related Software: Virtual Cell; Bio-PEPA; MAVisto; EMBOSS; MrBayes; ViennaRNA; … Main Fields: –
BNArray Software Authors: Xiaohui Chen, Ming Chen, Kaida Ning Cited in: 1 Publication (2010) Related Software: AutoNet Main Fields: –
BooleSim Software Authors: Bock M, Scharp T, Talnikar C, Klipp E. Cited in: 2 Publications (2015–2019) Related Software: GDSCalc; TURING; CoCalc; Docker; Ginsim; BoolNet; … Main Fields: –
GENeVis Software Authors: Westenberg, Michel A.; van Hijum, Sacha A.F.T.; Lulko, Andrzej T.; Kuipers, Oscar P.; Roerdink, Jos B.T.M. Cited in: 2 Publications (2008–2021) Related Software: node2vec; DeepWalk; graph2vec; TopoLayout; Prefuse; GVF Main Fields: (68U10-XX); (62M10-XX); (92C50-XX)
INLOCANDA Software Authors: Pio, Gianvito; Ceci, Michelangelo; Prisciandaro, Francesca; Malerba, Donato Cited in: 2 Publications (2020–2021) Related Software: IOTA; DeepWalk; ComiRNet; node2vec; ARACNE; word2vec; … Main Fields: (68T05-XX)
IntaRNA Software Authors: Wright PR, Georg J, Mann M, Sorescu DA, Richter AS, Lott S, Kleinkauf R, Hess WR, Backofen R Cited in: 2 Publications (2019–2020) Related Software: CopraRNA; NOMAD; GeneNetWeaver; Path2Models; SOSlib; LASSIE; … Main Fields: (92-06-XX); (92C42-XX); (92C40-XX)
MetNet Software Authors: Wurtele E, Li J, Diao L, Zhang H, Foster C, Fatland B, Dickerson J, Brown A, Cox Z, Cook D, Lee E, Hofmann H Cited in: 0 Publications Related Software: Cytoscape; Bioconductor; R; rattle; iSPlot; GTK+; … Main Fields: –
multistatepdscontrol Software Authors: Sordo Vieira, Luis; Laubenbacher, Reinhard C.; Murrugarra, David Cited in: 2 Publications (2020–2021) Related Software: CANA; GitHub; ADAM; Ginsim; Macaulay2 Main Fields: Biology and other natural sciences (92-XX)
NetBenchmark Software Authors: Bellot P, Olsen C, Salembier P, Oliveras-Vergés A, Meyer PE Cited in: 2 Publications (2019) Related Software: ARACNE; ITE; NOMAD; GeneNetWeaver; Path2Models; SOSlib; … Main Fields: –
PathCellNet Software Authors: Katanic D, Khan A, Thakar J Cited in: 2 Publications (2018) Related Software: SQUAD; ClueGO; gcrma; RedeR; STRINGdb; ANIMO; … Main Fields: –
SELANSI Software Authors: Pájaro M, Otero-Muras I, Vázquez C, Alonso AA Cited in: 2 Publications (2018–2019) Related Software: – Main Fields: –
YEASTRACT Software Authors: Teixeira MC et al Cited in: 2 Publications (2018–2020) Related Software: KEGG; GlobalMIT; BGRMI; ARACNE; MESS; G1DBN; … Main Fields: –
AutoNet Software Authors: Qu, Kun; Yesnik, Anastasia M.; Ortoleva, Peter J. Cited in: 1 Publication (2010) Related Software: BNArray Main Fields: (92C42-XX); (92C40-XX); (92D10-XX)
BoolSi Software Authors: Vladyslav Oles; Anton Kukushkin Cited in: 0 Publications Related Software: BoolNet; PlantSimLab; Ginsim; BioNetGen; Python Main Fields: –
CSI Software Authors: Penfold, Christopher A.; Shifaz, Ahmed; Brown, Paul E.; Nicholson, Ann; Wild, David L. Cited in: 1 Publication (2015) Related Software: XnView; Sante DICOM Viewer; DREAM4; Matlab Main Fields: (92-04-XX); (62-04-XX); (62G99-XX)
dynGENIE3 Software Authors: Huynh-Thu VA, Geurts P Cited in: 1 Publication (2019) Related Software: NOMAD; GeneNetWeaver; Path2Models; SOSlib; LASSIE; BioPreDyn-bench; … Main Fields: –
DYVIPAC Software Authors: Lan K. Nguyen, Andrea Degasperi, Philip Cotter, Boris N. Kholodenko Cited in: 0 Publications Related Software: SBW; LibSBMLSim; RunBioSimulations; PySCeS; SOSlib; LLVM; … Main Fields: –
expansion-network Software Authors: Réda, Clémence; Wilczyński, Bartek Cited in: 1 Publication (2020) Related Software: MaBoSS; REDfly; GitHub; Python; Ginsim; z3; … Main Fields: (92C42-XX); (92C40-XX)
GeneFriends Software Authors: van Dam, S.; Craig, T.; de Magalhaes, J. P. Cited in: 1 Publication (2020) Related Software: PLANEX; COXPRESdb; TGCnA; clusterProfiler; GitHub; KEGG; … Main Fields: –
GeneSPIDER Software Authors: Tjärnberg A, Morgan DC, Studham M, Nordling TEM, Sonnhammer ELL Cited in: 1 Publication (2019) Related Software: NOMAD; GeneNetWeaver; Path2Models; SOSlib; LASSIE; BioPreDyn-bench; … Main Fields: –
GENIE3 Software Authors: Van Anh Huynh-Thu, Sara Aibar, Pierre Geurts Cited in: 0 Publications Related Software: VCNet; edgeR; ARACNE; DEseq; JDINAC; DINGO; … Main Fields: –
grndata Software Authors: Pau Bellot, Catharina Olsen, Patrick E Meyer Cited in: 0 Publications Related Software: VCNet; edgeR; ARACNE; DEseq; JDINAC; DINGO; … Main Fields: –
Jimena Software Authors: Karl S, Dandekar T Cited in: 1 Publication (2018) Related Software: SQUAD; ClueGO; gcrma; RedeR; STRINGdb; ANIMO; … Main Fields: –
KINSOLVER Software Authors: Aleman-Meza, Boanerges; Yu, Yihai; Sch\"uttler, Heinz-Bernd; Arnold, Jonathan; Taha, Thiab R. Cited in: 1 Publication (2009) Related Software: Virtual Cell; JigCell; YSMP; MEG; STOCKS; MetaModel; … Main Fields: (92C40-XX); (92-04-XX); (92-08-XX)
maigesPack Software Authors: Esteves, Gustavo H.; Reis, Luiz F. L. Cited in: 1 Publication (2018) Related Software: R; sma; GSNCA; KEGG; WGCNA; Bioconductor Main Fields: (92C40-XX); (92C42-XX); (62P10-XX)
Mirsynergy Software Authors: Li, Y.; Liang, C.; Wong, K.C.; Luo, J.; Zhang, Z. Cited in: 1 Publication (2017) Related Software: GOstats Main Fields: –
NatalieQ Software Authors: El-Kebir, M.; Brandt, B.W.; Heringa, J.; Klau, G.W. Cited in: 1 Publication (2015) Related Software: L-GRAAL; MAGNA++; NETAL; HubAlign; STRING; KEGG; … Main Fields: –
PyPanda Software Authors: David G.P. van IJzendoorn, Kimberly Glass, John Quackenbush, Marieke L. Kuijjer Cited in: 0 Publications Related Software: NumPy Main Fields: –
QSSPN Software Authors: Fisher, C. P.; Plant, N. J.; Moore, J. B.; Kierzek, A. M Cited in: 1 Publication (2015) Related Software: – Main Fields: –
SeqNet Software Authors: Tyler Grimes, Somnath Datta Cited in: 0 Publications Related Software: VCNet; edgeR; ARACNE; DEseq; JDINAC; DINGO; … Main Fields: –
SiGN-SSM Software Authors: Tamada, Yoshinori; Yamaguchi, Rui; Imoto, Seiya; Hirose, Osamu; Yoshida, Ryo; Nagasaki, Masao; Miyano, Satoru Cited in: 0 Publications Related Software: – Main Fields: –
TRaCE+ Software Authors: Ud-Dean SMM, Heise S, Klamt S, Gunawan R Cited in: 1 Publication (2019) Related Software: NOMAD; GeneNetWeaver; Path2Models; SOSlib; LASSIE; BioPreDyn-bench; … Main Fields: –
MetaDCN Software Authors: L. Zhu, Y. Ding, C. Y. Chen et al. Cited in: 0 Publications Related Software: – Main Fields: –
pandaR Software Authors: Dan Schlauch, Joseph N. Paulson, Albert Young, John Quackenbush, Kimberly Glass Cited in: 0 Publications Related Software: – Main Fields: –
parmigene Software Authors: Gabriele Sales, Chiara Romualdi Cited in: 0 Publications Related Software: – Main Fields: –