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Found 427 Software Packages (Results 1–100)

SVMlight

Software Authors:   Thorsten Joachims
Referenced in: 209 Publications (2000–2022)
Related Software: LIBSVM; UCI-ml; SVMTorch; Matlab; GPDT; CONV_QP; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Computer science (68-XX)

APCluster

Software Authors:   Brendan J. Frey; Delbert Dueck; Ulrich Bodenhofer , Johannes Palme , Chrats Melkonian , Andreas Kothmeier
Referenced in: 90 Publications (2007–2022)
Related Software: apcluster; UCI-ml; clusfind; AS 136; R; ElemStatLearn; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

APBS

Software Authors:   Nathan Baker; J. Andrew McCammon; Michael Holst
Referenced in: 91 Publications (2001–2022)
Related Software: MIBPB; tabipb; CHARMM; TABI; PDB2PQR; PBEQ-Solver; …
Main Fields: Partial differential equations (35-XX); Numerical analysis (65-XX); Optics, electromagnetic theory (78-XX)

Graphviz

Software Authors:   Ellson, John; Gansner, Emden; Koutsofios, Lefteris; North, Stephen C.; Woodhull, Gordon
Referenced in: 70 Publications (2001–2022)
Related Software: Dynagraph; R; Python; CPLEX; GAP; Rgraphviz; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

edgeR

Software Authors:   Mark D. Robinson; Davis J. McCarthy; Gordon K. Smyth
Referenced in: 49 Publications (2011–2022)
Related Software: Bioconductor; R; DEseq; Voom; BaySeq; TopHat; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Numerical analysis (65-XX)

COSA

Software Authors:   Friedman, Jerome H.; Meulman, Jacqueline J.
Referenced in: 49 Publications (2003–2022)
Related Software: UCI-ml; sparcl; R; mclust; clusfind; Silhouettes; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Computer science (68-XX)

Cd-hit

Software Authors:   Weizhong Li, Adam Godzik
Referenced in: 32 Publications (2007–2021)
Related Software: Cell-PLoc; LIBSVM; BLAST; PSI-BLAST; UniProt; iRSpot-PseDNC; …
Main Fields: Algebraic geometry (14-XX); Algebraic topology (55-XX); Statistics (62-XX)

Taverna

Software Authors:   Oinn, T.; Addis, M.; Ferris, J.; Marvin, D.; Senger, M.; Greenwood, M.; Carver, T.; Glover, K.; Pocock, M. R.; Wipat, A.; Li, P.
Referenced in: 8 Publications (2005–2019)
Related Software: Pegasus; Java CoG Kit; BioMOBY; Globus Toolkit; YAWL; Triana; …
Main Fields: History and biography (01-XX); Statistics (62-XX); Computer science (68-XX)

Pse-in-One

Software Authors:   Liu, B.; Liu, F.; Wang, X.; Chen, J.; Fang, L.; Chou, K. -C.:
Referenced in: 41 Publications (2015–2019)
Related Software: iRSpot-PseDNC; PseKNC; iPro54-PseKNC; pLoc-mEuk; iRNA-PseColl; pLoc-mAnimal; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

iLoc-Euk

Software Authors:   Chou, K. -C.; Wu, Z. -C.; Xiao, X.
Referenced in: 37 Publications (2011–2019)
Related Software: iLoc-Hum; Cell-PLoc; iLoc-Virus; Plant-mPLoc; iLoc-Gpos; LIBSVM; …
Main Fields: Harmonic analysis on Euclidean spaces (42-XX); Statistics (62-XX); Computer science (68-XX)

DIALIGN

Software Authors:   B. Morgenstern
Referenced in: 23 Publications (2001–2022)
Related Software: ClustalW; MUSCLE; T-coffee; MAFFT; ProbCons; Balibase; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Computer science (68-XX)

CloseGraph

Software Authors:   X. Yan; J. Han
Referenced in: 19 Publications (2005–2020)
Related Software: gSpan; CLOSET; CMAR; nauty; CloSpan; PrefixSpan; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

Infer.NET

Software Authors:   Microsoft Research; Minka, T.; Winn, J.; Guiver, G.; Kannan, A.
Referenced in: 22 Publications (2011–2022)
Related Software: R; Stan; BUGS; PRMLT; WinBUGS; SemiPar; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Computer science (68-XX)

iRSpot-EL

Software Authors:   Liu, B.; Wang, S.; Long, R.; Chou, K. -C.
Referenced in: 29 Publications (2017–2022)
Related Software: iRNA-PseColl; 2L-piRNA; pLoc-mEuk; pLoc-mAnimal; iPromoter-2L; iRNA-AI; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

iPTM-mLys

Software Authors:   Qiu, W. -R.; Sun, B. -Q.; Xiao, X.; Xu, Z. -C.; Chou, K. -C.
Referenced in: 26 Publications (2016–2019)
Related Software: Pse-in-One; iRNA-PseColl; pLoc-mAnimal; pSuc-Lys; pLoc-mEuk; iRSpot-PseDNC; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

CFinder

Software Authors:   Balázs Adamcsek; Gergely Palla; Illés J. Farkas; Imre Derényi; Tamás Vicsek
Referenced in: 16 Publications (2006–2020)
Related Software: MCODE; BioGRID; R; Cytoscape; KEGG; igraph; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

2L-piRNA

Software Authors:   Liu, B.; Yang, F.; Chou, K.-C.
Referenced in: 25 Publications (2017–2019)
Related Software: iRNA-PseColl; iRSpot-EL; pLoc-mEuk; Pse-in-One; pLoc-mAnimal; iDNA6mA-PseKNC; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

Reactome

Software Authors:   G. Joshi-Tope M. Gillespie; I. Vastrik; P. D'Eustachio; E. Schmidt; B. de Bono; B. Jassal; G.R. Gopinath; G.R. Wu; L. Matthews; S. Lewis; E. Birney; L. Stein
Referenced in: 13 Publications (2008–2022)
Related Software: KEGG; Bioconductor; MetaCyc; Celldesigner; BioGRID; Cytoscape; …
Main Fields: Combinatorics (05-XX); Partial differential equations (35-XX); Statistics (62-XX)

bioperl

Software Authors:   Stajich, J.E., et al.
Referenced in: 10 Publications (2006–2021)
Related Software: PERL; Biopython; ClustalW; BLAST; R; UniProt; …
Main Fields: General and overarching topics; collections (00-XX); Combinatorics (05-XX); Statistics (62-XX)

iPromoter-2L

Software Authors:   Liu, B.; Yang, F.; Huang, D. S.
Referenced in: 22 Publications (2018–2019)
Related Software: iRSpot-EL; iRNA-PseColl; pLoc-mAnimal; pLoc-mEuk; iDNA6mA-PseKNC; 2L-piRNA; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

FatiGO

Software Authors:   Al-Shahrour, F.; Diaz-Uriarte, R.; Dopazo, J.
Referenced in: 15 Publications (2004–2015)
Related Software: GOstat; R; Bioconductor; KEGG; GOTM; GO-TermFinder; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Computer science (68-XX)

iDNA6mA-PseKNC

Software Authors:   Feng, P.; Yang, H.; Ding, H.; Lin, H.; Chen, W.; Chou, K.-C.
Referenced in: 21 Publications (2018–2019)
Related Software: iRNA-PseColl; iPromoter-2L; iRSpot-EL; pLoc-mEuk; pLoc-mAnimal; 2L-piRNA; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

iEnhancer-2L

Software Authors:   Bin Liu; Longyun Fang; Ren Long; Xun Lan; Kuo-Chen Chou
Referenced in: 21 Publications (2016–2019)
Related Software: pLoc-mAnimal; pSuc-Lys; Pse-in-One; iPromoter-2L; iRSpot-EL; iRNA-PseColl; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

Biopython

Software Authors:   Cock, P. J. A.; Antao, T.; Chang, J. T.; Chapman, B. A.; Cox, C. J.; Dalke, A.; Friedberg, I.; Hamelryck, T.; Kauff, F.; Wilczynski, B.; De Hoon, M. J.
Referenced in: 7 Publications (2009–2019)
Related Software: Python; bioperl; BioJava; DendroPy; TRANSFAC; UniProt; …
Main Fields: General and overarching topics; collections (00-XX); Mathematical logic and foundations (03-XX); Statistics (62-XX)

ProTDB

Software Authors:   A. Nierrman, H.V. Jagadish
Referenced in: 12 Publications (2005–2018)
Related Software: ProbView; PSQL; XPath; TAX; XSEarch; XQuery; …
Main Fields: Computer science (68-XX)

iLoc-Plant

Software Authors:   Wu, Z. -C.; Xiao, X.; Chou, K. -C.
Referenced in: 18 Publications (2012–2019)
Related Software: iLoc-Virus; iLoc-Euk; iLoc-Hum; iLoc-Gpos; Cell-PLoc; iLoc-Animal; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

InterProScan

Software Authors:   E. Quevillon, V. Silventoinen, S. Pillai, N. Harte, N. Mulder, R. Apweiler, R. Lopez
Referenced in: 6 Publications (2009–2022)
Related Software: BLAST; PSI-BLAST; UniProt; EasyGene; PROSITE; MultiLoc2; …
Main Fields: General and overarching topics; collections (00-XX); Probability theory and stochastic processes (60-XX); Computer science (68-XX)

LogitBoost

Software Authors:   Chang, Yuan-Chin Ivan; Huang, Yufen; Huang, Yu-Pai
Referenced in: 17 Publications (2006–2020)
Related Software: iRSpot-PseDNC; iProt-Sub; iNitro-Tyr; PseKNC; LIBSVM; 2L-piRNA; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Computer science (68-XX)

iPhos-PseEvo

Software Authors:   Qiu, W.R.; Sun, B.Q.; Xiao, X.
Referenced in: 17 Publications (2016–2019)
Related Software: iRNAm5C-PseDNC; pLoc-mEuk; Pse-in-One; 2L-piRNA; iRSpot-EL; iRNA-PseColl; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

SynTReN

Software Authors:   Van den Bulcke, T., Van Leemput, K., Naudts, B., van Remortel, P., Ma, H., Verschoren, A., De Moor, B.: Marchal, K.
Referenced in: 14 Publications (2009–2021)
Related Software: ARACNE; glasso; R; minet; igraph; GeneNetWeaver; …
Main Fields: General and overarching topics; collections (00-XX); Combinatorics (05-XX); Statistics (62-XX)

MemHyb

Software Authors:   Hayat, Maqsood; Khan, Asifullah
Referenced in: 15 Publications (2012–2019)
Related Software: Memtype-2L; iLoc-Hum; iRSpot-PseDNC; Pse-in-One; iLoc-Euk; iDNA-Methyl; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

mpiBLAST

Software Authors:   –
Referenced in: 8 Publications (2004–2019)
Related Software: BLAST; Globus Toolkit; PSI-BLAST; ClustalW; EMBOSS; UniProt; …
Main Fields: Computer science (68-XX); Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

TM-align

Software Authors:   Zhang, Y., Skolnick, J.
Referenced in: 9 Publications (2009–2021)
Related Software: BLAST; PSI-BLAST; ClustalW; MAMMOTH; SSAP; Gephi; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

ExPASy

Software Authors:   Gasteiger, E.; Gattiker, A.; Hoogland, C.; Ivanyi, I.; Appel, R. D.; Bairoch, A
Referenced in: 10 Publications (2006–2020)
Related Software: MODELLER; BLAST; PSI-BLAST; R; UniProt; PROCHECK; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

iProt-Sub

Software Authors:   Song J, Wang Y, Li F, Akutsu T, Rawlings ND, Webb GI, Chou KC
Referenced in: 14 Publications (2018–2019)
Related Software: iPromoter-2L; iRNA-PseColl; Pse-in-One; 2L-piRNA; iRSpot-EL; pLoc-mAnimal; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

iRNA-2methyl

Software Authors:   Qiu, W.R.; Jiang, S.Y.; Sun, B.Q.; Xia, X.
Referenced in: 14 Publications (2017–2019)
Related Software: iRNA-PseColl; Pse-in-One; 2L-piRNA; iSuc-PseOpt; iRSpot-EL; pLoc-mEuk; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

SecretP

Software Authors:   Yu, L.; Guo, Y.; Li, Y.; Li, G.; Li, M.; Luo, J.; Xiong, W.; Qin, W.
Referenced in: 14 Publications (2010–2013)
Related Software: Cell-PLoc; Euk-mPLoc; iLoc-Virus; Plant-mPLoc; iLoc-Euk; GPCR-2L; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

BioJava

Software Authors:   Andreas Prlic; Andrew Yates; Spencer E. Bliven; Peter W. Rose; Julius Jacobsen; Peter V. Troshin; Mark Chapman; Jianjiong Gao; Chuan Hock Koh; Sylvain Foisy; Richard Holland; Gediminas Rimsa; Michael L. Heuer; H. Brandstatter-Muller; Philip E. Bourne; Scooter Willis
Referenced in: 5 Publications (2009–2017)
Related Software: Biopython; bioperl; MMTK; ProDy; Python; Taverna; …
Main Fields: General and overarching topics; collections (00-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

FABIA

Software Authors:   Sepp Hochreiter, Ulrich Bodenhofer, Martin Heusel, Andreas Mayr, Andreas Mitterecker, Adetayo Kasim, Tatsiana Khamiakova, Suzy Van Sanden, Dan Lin, Willem Talloen, Luc Bijnens, Hinrich W.H. Göhlmann, Ziv Shkedy, and Djork-Arné Clevert
Referenced in: 12 Publications (2013–2022)
Related Software: R; BicPAMS; BicNET; BicAT; Matlab; LAS; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

iRO-3wPseKNC

Software Authors:   Liu, B.; Weng, F.; Huang, D.-S.; Chou, K.-C.
Referenced in: 13 Publications (2018–2019)
Related Software: iRNA-PseColl; iDNA6mA-PseKNC; iRNA-3typeA; iPromoter-2L; iRSpot-EL; pLoc-mAnimal; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

iEnhancer-EL

Software Authors:   Liu, B.; Li, K.; Huang, D.-S.; Chou, K.-C.
Referenced in: 11 Publications (2018–2019)
Related Software: pLoc-mGneg; iRO-3wPseKNC; iDNA6mA-PseKNC; iRNA-3typeA; iPromoter-2L; iRSpot-EL; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

LOCSVMPSI

Software Authors:   Xie, D.; Li, A.; Wang, M.; Fan, Z.; Feng, H.
Referenced in: 7 Publications (2008–2016)
Related Software: ESLpred; Cell-PLoc; Esub8; WoLF PSORT; Euk-mPLoc; Euk-PLoc; …
Main Fields: Harmonic analysis on Euclidean spaces (42-XX); Statistics (62-XX); Computer science (68-XX)

maSigPro

Software Authors:   Conesa, A.; Nueda, M. J.; Talon, M.
Referenced in: 6 Publications (2009–2021)
Related Software: Bioconductor; EDGE; edgeR; R; DESeq2; ptmixed; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

Bio2RDF

Software Authors:   Belleau, Franc cois; Tourigny, Nicole; Good, Benjamin; Morissette, Jean
Referenced in: 3 Publications (2010–2019)
Related Software: KEGG; DBpedia; ArrayExpress; STRING; PubChem; PL-ranking; …
Main Fields: Statistics (62-XX); Computer science (68-XX)

DIYABC

Software Authors:   Cornuet JM, Pudlo P, Veyssier J, Dehne-Garcia A, Gautier M, Leblois R, Marin JM, Estoup A
Referenced in: 7 Publications (2012–2022)
Related Software: abcrf; R; abc; ABrox; abctools; ABCtoolbox; …
Main Fields: Integral equations (45-XX); Probability theory and stochastic processes (60-XX); Statistics (62-XX)

GEOquery

Software Authors:   Sean D, Meltzer PS
Referenced in: 7 Publications (2016–2021)
Related Software: R; Bioconductor; shiny; WEKA; adaptMT; AdaPT; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Computer science (68-XX)

iDHS-EL

Software Authors:   Liu, B.; Long, R.; Chou, K. -C.
Referenced in: 10 Publications (2016–2019)
Related Software: Pse-in-One; pSuc-Lys; Prnam-PC; iSuc-PseOpt; iEnhancer-2L; iRSpot-PseDNC; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

iMiRNA-PseDPC

Software Authors:   Liu, B.; Fang, L.; Liu, F.; Wang, X.; Chou, K. -C.
Referenced in: 10 Publications (2015–2019)
Related Software: Pse-in-One; PseKNC; iPPI-Esml; iAMP-2L; iDNA-Methyl; iPro54-PseKNC; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

PREvaIL

Software Authors:   Song, Jiangning; Li, Fuyi; Takemoto, Kazuhiro; Haffari, Gholamreza; Akutsu, Tatsuya; Chou, Kuo-Chen; Webb, Geoffrey I.
Referenced in: 10 Publications (2018–2019)
Related Software: iDNA6mA-PseKNC; iRNA-PseColl; pLoc-mAnimal; 2L-piRNA; iPromoter-2L; iRSpot-EL; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

PSICO

Software Authors:   Krippahl, Ludwig; Barahona, Pedro
Referenced in: 9 Publications (2002–2017)
Related Software: COCONUT; GLOPTLAB; BARON; INTLAB; ICOS; InC++; …
Main Fields: Numerical analysis (65-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

T-REX

Software Authors:   Boc, A., Diallo, A.B., Makarenkov, V.
Referenced in: 9 Publications (2006–2022)
Related Software: RIATA-HGT; SplitsTree; IcyTree; Dendroscope; ggplot2; Mesquite; …
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

apTreeshape

Software Authors:   Nicolas Bortolussi, Michael Blum, Eric Durand, Olivier Francois, Odile Maliet
Referenced in: 7 Publications (2007–2020)
Related Software: R; ape; AUGEM; adaptMCMC; MrBayes; GEIGER; …
Main Fields: Combinatorics (05-XX); Probability theory and stochastic processes (60-XX); Statistics (62-XX)

CDK

Software Authors:   Steinbeck, C., Han, Y., Kuhn, S., Horlacher, O., Luttmann, E., Willighagen, E.
Referenced in: 2 Publications (2020–2021)
Related Software: ChEMBL; JChemPaint; UniProt; Bioclipse; Taverna; PubChem PUG; …
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

GOTM

Software Authors:   Bing Zhang, Denise Schmoyer, Stefan Kirov; Jay Snoddy
Referenced in: 6 Publications (2005–2014)
Related Software: FatiGO; KEGG; GOstat; DAVID; Onto-Tools; GOToolBox; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

ProActive

Software Authors:   Inria Sophia Antipolis
Referenced in: 6 Publications (2002–2019)
Related Software: AmbientTalk; ABS; Creol; Multilisp; IC2D; ABCL; …
Main Fields: Numerical analysis (65-XX); Computer science (68-XX); Geophysics (86-XX)

Proteinortho

Software Authors:   Lechner, M., Findeiß, S., Steiner, L., Manja, M., Stadler, P., Prohaska, S.
Referenced in: 8 Publications (2013–2021)
Related Software: OrthoMCL; OMA; eggNOG; PADRE; Genetree; S-Cluster++; …
Main Fields: General and overarching topics; collections (00-XX); Combinatorics (05-XX); Computer science (68-XX)

SABmark

Software Authors:   Walle, I.V., Lasters, I., Wyns, L.
Referenced in: 4 Publications (2013–2017)
Related Software: MUSCLE; ClustalW; OXBench; Kalign; ProbCons; Balibase; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)

TAMBIS

Software Authors:   Stevens, R.; Baker, P.; Bechhofer, S.; Ng, G.; Jacoby, A.; Paton, N.W.; Goble, C.A.; Brass, A.
Referenced in: 2 Publications (2001–2006)
Related Software: UniProt; KEGG; caGrid; Soap; Eiffel; i*; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

Chameleon

Software Authors:   Sang-Min P, Jair-Hoom K.
Referenced in: 2 Publications (2008–2013)
Related Software: Globus Toolkit; Java CoG Kit; OptorSim; Pegasus; TGFF; ABC; …
Main Fields: Computer science (68-XX); Operations research, mathematical programming (90-XX)

ELM

Software Authors:   Pål Puntervoll, Rune Linding, Christine Gemünd, et. al.
Referenced in: 1 Publication (2016)
Related Software: PROSITE; Cd-hit; Phospho.ELM; IUPred; GlobPlot; R; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

iLoc-lncRNA

Software Authors:   Zhen-Dong Su, Yan Huang, Zhao-Yue Zhang, Ya-Wei Zhao, Dong Wang, Wei Chen, Kuo-Chen Chou, Hao Lin
Referenced in: 8 Publications (2018–2019)
Related Software: pLoc-mEuk; iRO-3wPseKNC; 2L-piRNA; iDNA6mA-PseKNC; iRNA-3typeA; pLoc-mGneg; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

KEGGgraph

Software Authors:   Jitao David Zhang; Stefan Wiemann
Referenced in: 7 Publications (2011–2015)
Related Software: Bioconductor; KEGG; Reactome; igraph; clipper; graphite; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Biology and other natural sciences (92-XX)

OACC

Software Authors:   Soler-Toscano F, Zenil H, Delahaye J-P, Gauvrit N
Referenced in: 8 Publications (2013–2022)
Related Software: acss; OEIS; DIMACS
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

ParFE

Software Authors:   M. Sala, U. Mennel, P. Arbenz, H. van Lenthe, R. Müller
Referenced in: 8 Publications (2008–2015)
Related Software: LAM-MPI; HDF5; Amesos; IFPACK; METIS; PETSc; …
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Mechanics of deformable solids (74-XX)

POSSUM

Software Authors:   Wang, J.; Yang, B.; Revote, J.; Leier, A.; Marquez-Lago, T.T.; Web.; Lithgow, T.
Referenced in: 8 Publications (2017–2019)
Related Software: 2L-piRNA; iRSpot-EL; iRNA-PseColl; pLoc-mAnimal; PseKNC; Pse-in-One; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

Avogadro

Software Authors:   Marcus D Hanwell, Donald E Curtis, David C Lonie, Tim Vandermeersch, Eva Zurek, Geoffrey R Hutchison
Referenced in: 6 Publications (2011–2018)
Related Software: Open Babel; VASP; XtalOpt; GULP; VMD; GAMESS; …
Main Fields: Group theory and generalizations (20-XX); Computer science (68-XX); Quantum theory (81-XX)

3DCoffee

Software Authors:   O. O’Sullivan, K. Suhre, C. Abergel, D. G. Higgins, C. Notredame
Referenced in: 5 Publications (2005–2016)
Related Software: ClustalW; ProbCons; T-coffee; MUSCLE; MAFFT; SABmark; …
Main Fields: History and biography (01-XX); Statistics (62-XX); Numerical analysis (65-XX)

Oncomine

Software Authors:   Rhodes DR, Kalyana-Sundaram S, Mahavisno V et al
Referenced in: 3 Publications (2011–2016)
Related Software: GeneSigDB; Bioconductor; ArrayExpress; Galaxy; ROAST; featureCounts; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Biology and other natural sciences (92-XX)

PSICOV

Software Authors:   David T. Jones, Daniel W. A. Buchan, Domenico Cozzetto, Massimiliano Pontil
Referenced in: 6 Publications (2014–2021)
Related Software: R; Pfam; BLAST; PSI-BLAST; NNcon; bnlearn; …
Main Fields: Statistics (62-XX); Statistical mechanics, structure of matter (82-XX); Operations research, mathematical programming (90-XX)

ScalaBLAST

Software Authors:   Oehmen, C.; Nieplocha, Jarek
Referenced in: 4 Publications (2008–2020)
Related Software: BLAST; k-means++; AS 136; PSI-BLAST; mpiBLAST; Silhouettes; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

BART-BMA

Software Authors:   Hernández, Belinda; Raftery, Adrian E.; Pennington, Stephen R.; Parnell, Andrew C.
Referenced in: 6 Publications (2018–2022)
Related Software: BartPy; R; bartMachine; randomForest; tsbart; GitHub; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Computer science (68-XX)

bioNMF

Software Authors:   Montano A, Saez P, Chagoyen M, Tirado F, Carazo JM, Marqui RD
Referenced in: 5 Publications (2008–2020)
Related Software: FABIA; DAVID; Wenxiang; MEGAN; ONE; RAST; …
Main Fields: Linear and multilinear algebra; matrix theory (15-XX); Statistics (62-XX); Numerical analysis (65-XX)

BVSNLP

Software Authors:   Amir Nikooienejad
Referenced in: 5 Publications (2019–2021)
Related Software: R; EMVS; glmnet; survAUC; CRAN; BayesVarSel; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX)

Carpenter

Software Authors:   F. Pan, G. Cong, A.K.H. Tung, J. Yang, M.J. Zaki
Referenced in: 3 Publications (2009–2014)
Related Software: CLOSET; COBBLER; CMAR; FARMER; RP-Tree; TitanicOR; …
Main Fields: Computer science (68-XX)

DIAL

Software Authors:   F. Ferrè; Y. Ponty; W. A. Lorenz; Peter Clote
Referenced in: 3 Publications (2008–2015)
Related Software: ARTS; MAMMOTH; FRASS; iPARTS; FR3D; SARSA; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

HierNMF2

Software Authors:   Da Kuang, Haesun Park
Referenced in: 6 Publications (2015–2022)
Related Software: SymNMF; SmallK; RCV1; MALLET; CLUTO; SNAP; …
Main Fields: Linear and multilinear algebra; matrix theory (15-XX); Numerical analysis (65-XX); Operations research, mathematical programming (90-XX)

KMC

Software Authors:   Deorowicz, S., Kokot, M., Grabowski, S., Debudaj, A
Referenced in: 6 Publications (2016–2022)
Related Software: Velvet; GitHub; Turtle; Gerbil; Winnowing; Minimap2; …
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

MEIGO

Software Authors:   Egea JA, Henriques D, Cokelaer T, Villaverde AF, MacNamara A, Danciu DP, Banga JR, Saez-Rodriguez J.
Referenced in: 2 Publications (2010–2019)
Related Software: COPASI; R; AMIGO; tellurium; BioNetGen; PyBioNetFit; …
Main Fields: Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

Nextstrain

Software Authors:   Hadfield J, Megill C, Bell SM, Huddleston J, Potter B, Callender C, Sagulenko P, Bedford T, Neher RA
Referenced in: 5 Publications (2019–2022)
Related Software: adapref; phylodyn; BEAST; GMRFLib; Stan; BEAGLE; …
Main Fields: Dynamical systems and ergodic theory (37-XX); Probability theory and stochastic processes (60-XX); Statistics (62-XX)

PseDNA-Pro

Software Authors:   Liu, B.; Xu, J.; Fan, S.; Xu, R.; Zhou, J.; Wang, X.
Referenced in: 6 Publications (2015–2019)
Related Software: iRSpot-PseDNC; Pse-in-One; repDNA; PseKNC; iMiRNA-PseDPC; iAMP-2L; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

PSNO

Software Authors:   Zhang, J.; Zhao, X.; Sun, P.; Ma, Z.
Referenced in: 6 Publications (2015–2019)
Related Software: iHyd-PseAAC; iNitro-Tyr; iSNO-PseAAC; iMethyl-PseAAC; pLoc-mHum; iRNA-2methyl; …
Main Fields: Computer science (68-XX); Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

SNPHarvester

Software Authors:   Yang, C.; He, Z.; Wan, X.; Yang, Q.; Xue, H.; Yu, W.
Referenced in: 4 Publications (2014–2021)
Related Software: epiACO; DESeeker; GWAS Catalog; MACOED; GAMETES; Octave; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

SPARQ2L

Software Authors:   Kemafor Anyanwu; Angela Maduko; Amit Sheth
Referenced in: 4 Publications (2009–2017)
Related Software: SPARQL; Jena; XPath; nSPARQL; Oracle; HPRD; …
Main Fields: Mathematical logic and foundations (03-XX); Computer science (68-XX)

VARNA

Software Authors:   K. Darty, A. Denise. Y. Ponty
Referenced in: 4 Publications (2012–2022)
Related Software: ViennaRNA; Rfam; R2R; jViz.Rna; PseudoViewer3; Infernal; …
Main Fields: General and overarching topics; collections (00-XX); Combinatorics (05-XX); Calculus of variations and optimal control; optimization (49-XX)

Bio++

Software Authors:   Dutheil J, Boussau B
Referenced in: 3 Publications (2011–2019)
Related Software: SplitsTree; MrBayes; MulRF; iGTP; ExaBayes; pIQPNNI; …
Main Fields: General and overarching topics; collections (00-XX); Combinatorics (05-XX); Operations research, mathematical programming (90-XX)

BioRuby

Software Authors:   Katayama, Toshiaki; Kawashima, Shuichi; Goto, Naohisa; Nakao, Mitsuteru C.; Okuji, Yoshinori K.; Kanehisa, Minoru; Dunker, A.K.; Konagaya, A.; Miyano, S.; Takagi, T.
Referenced in: 1 Publication (2019)
Related Software: bioperl; Biopython; Omics Pipe; Anaconda; IPython; PyPI; …
Main Fields: Biology and other natural sciences (92-XX)

Bismark

Software Authors:   Krueger, F.; S. Andrews
Referenced in: 4 Publications (2016–2021)
Related Software: Bowtie 2; BSMAP; BS Seeker; STAR; methylKit; Trimmomatic; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Computer science (68-XX)

Cellnoptr

Software Authors:   Terfve, C. D. A.; Cokelaer, T.; Henriques, D.; Macnamara, A.; Gonçalves, E.; Morris, M.; Van Iersel, M.; Lauffenburger, D. A.; Saez-Rodriguez, J.
Referenced in: 2 Publications (2015–2018)
Related Software: R; BoolNet; Graphviz; CellNOpt; KEGG; Pint; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

Engauge Digitizer

Software Authors:   Mark Mitchell
Referenced in: 5 Publications (2012–2022)
Related Software: NDSPMHD; SPHERA; SSA; CMA-ES; R
Main Fields: Statistics (62-XX); Computer science (68-XX); Mechanics of deformable solids (74-XX)

FARMER

Software Authors:   G. Cong, A.K.H. Tung, X. Xu, F. Pan, J. Yang
Referenced in: 4 Publications (2009–2015)
Related Software: Carpenter; COBBLER; C4.5; RP-Tree; TitanicOR; BLOSOM; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Computer science (68-XX)

GRIMM

Software Authors:   Tesler G
Referenced in: 5 Publications (2009–2019)
Related Software: MrBayes; PAUP*; S-Cluster++; SplitsTree; MCScanX; CYNTENATOR; …
Main Fields: General and overarching topics; collections (00-XX); Combinatorics (05-XX); Computer science (68-XX)

Hy3S

Software Authors:   H. Salis, V. Sotiropoulos, Y. N. Kaznessis
Referenced in: 5 Publications (2015–2019)
Related Software: COPASI; DASSL; URDME; Bio-PEPA; GreatSPN
Main Fields: Ordinary differential equations (34-XX); Probability theory and stochastic processes (60-XX); Numerical analysis (65-XX)

IntelliGEN

Software Authors:   Kochut, Krys; Arnold, Jonathan; Sheth, Amit; Miller, John; Kraemer, Eileen; Arpinar, Budak; Cardoso, Jorge
Referenced in: 4 Publications (2003–2012)
Related Software: Woflan; JigCell; Virtual Cell; YSMP; MEG; STOCKS; …
Main Fields: Computer science (68-XX); Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

MatInspector

Software Authors:   Cartharius K, Frech K, Grote K, Klocke B, Haltmeier M, Klingenhoff A, Frisch M, Bayerlein M, Werner T
Referenced in: 4 Publications (2006–2009)
Related Software: JASPAR; TRANSFAC; gNCA; COXPRESdb; ArrayExpress; Cytoscape; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX); Information and communication theory, circuits (94-XX)

MC2

Software Authors:   Robin Donaldson
Referenced in: 4 Publications (2010–2017)
Related Software: PRISM; Ymer; MRMC; COSMOS; MARCIE; Gecode; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

MIMIX

Software Authors:   Neal S. Grantham, Brian J. Reich, Elizabeth T. Borer, Kevin Gross
Referenced in: 5 Publications (2019–2020)
Related Software: edgeR; Bioconductor; PoiClaClu; PhyloScan; Julia; BayesDA; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

PSMIX

Software Authors:   Wu, B.; Liu, N.; Zhao, H.
Referenced in: 4 Publications (2009–2015)
Related Software: Frappe; STRUCTURE; BGLR; vegan; R; ANCESTRYMAP; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

PSoL

Software Authors:   Wang C., Ding C., Meraz R.F., Holbrook S.R.
Referenced in: 2 Publications (2008–2015)
Related Software: LIBSVM; PLMLA; GPS-YNO2; iSNO-PseAAC; Cd-hit; Cell-PLoc; …
Main Fields: Biology and other natural sciences (92-XX)

Quokka

Software Authors:   Li, F.; Li, C.; Marquez-Lago, T. T.; Leier, A.; Akutsu, T.; Purcell, A. W.; Ian Smith, A.; Lithgow, T.; Daly, R. J.; Song, J.
Referenced in: 5 Publications (2018–2019)
Related Software: pLoc-mHum; iKcr-PseEns; pLoc-mGneg; pLoc-mAnimal; iRSpot-Pse6NC; iRO-3wPseKNC; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

REDfly

Software Authors:   Halfon M, Gallo S, Bergman C
Referenced in: 2 Publications (2019–2020)
Related Software: R; expansion-network; MaBoSS; GitHub; Python; Ginsim; …
Main Fields: Biology and other natural sciences (92-XX)