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Found 207 Software Packages (Results 1–100)

UniProt

Software Authors:   The UniProt Consortium; Apweiler, R.; Bairoch, A.; Wu, C. H.; Barker, W. C.; Boeckmann, B.; Ferro, S.; Gasteiger, E.; Huang, H.; Lopez, R.; Magrane, M.; Martin, M. J.; Natale, D. A.; O’donovan, C.; Redaschi, N.; Yeh, L. S.
Referenced in: 70 Publications (2004–2022)
Related Software: BLAST; PSI-BLAST; KEGG; Pfam; Cd-hit; ClustalW; …
Main Fields: Combinatorics (05-XX); Probability theory and stochastic processes (60-XX); Statistics (62-XX)

MUMMER

Software Authors:   S. Kurtz, A. Phillippy, A.L. Delcher, M. Smoot, M. Shumway, C. Antonescu, S.L. Salzberg
Referenced in: 29 Publications (2003–2022)
Related Software: LAGAN; REPuter; BLASTZ; PatternHunter; AVID; DIALIGN; …
Main Fields: General and overarching topics; collections (00-XX); Combinatorics (05-XX); Computer science (68-XX)

BioProspector

Software Authors:   Liu, X., Brutlag, D., Liu, J.
Referenced in: 21 Publications (2002–2013)
Related Software: TRANSFAC; JASPAR; WebLogo; CisModule; PhyME; TEIRESIAS; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Numerical analysis (65-XX)

DESeq2

Software Authors:   Michael Love, Constantin Ahlmann-Eltze, Kwame Forbes, Simon Anders, Wolfgang Huber
Referenced in: 26 Publications (2015–2022)
Related Software: Bioconductor; edgeR; R; DEseq; Voom; BaySeq; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Numerical analysis (65-XX)

E-CELL

Software Authors:   M Tomita, K Hashimoto, K Takahashi, T S Shimizu,Y Matsuzaki ,F Miyoshi, K Saito S Tanida,K Yugi,J C Venter; C A Hutchison
Referenced in: 18 Publications (2003–2019)
Related Software: GEPASI; KEGG; Virtual Cell; SCAMP; COPASI; MCELL; …
Main Fields: Mathematical logic and foundations (03-XX); Probability theory and stochastic processes (60-XX); Numerical analysis (65-XX)

TopHat

Software Authors:   Kim D, Pertea G, Trapnell C et al
Referenced in: 20 Publications (2011–2021)
Related Software: Bioconductor; edgeR; R; KEGG; STAR; RSEM; …
Main Fields: General and overarching topics; collections (00-XX); Probability theory and stochastic processes (60-XX); Statistics (62-XX)

Bowtie 2

Software Authors:   Langmead, B., S. L. Salzberg
Referenced in: 19 Publications (2015–2022)
Related Software: BWA; Bismark; GATK; PatternHunter; Soap; Python; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

GATK

Software Authors:   A. McKenna, M. Hanna, E. Banks et al.
Referenced in: 16 Publications (2012–2021)
Related Software: Samtools; Trimmomatic; R; BWA; Bowtie 2; FastQC; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Computer science (68-XX)

SPAdes

Software Authors:   Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A. Gurevich, Mikhail Dvorkin, Alexander S. Kulikov, Valery M. Lesin, Sergey I. Nikolenko, Son Pham, Andrey D. Prjibelski, Alexey V. Pyshkin, Alexander V. Sirotkin, Nikolay Vyahhi, Glenn Tesler, Max A. Alekseyev, Pavel A. Pevzner
Referenced in: 17 Publications (2015–2022)
Related Software: Velvet; IDBA-UD; IDBA; ABySS; GAGE; MEGAHIT; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

SHRiMP

Software Authors:   Rumble SM, Lacroute P, Dalca AV, Fiume M, Sidow A, Brudno M
Referenced in: 10 Publications (2010–2017)
Related Software: PatternHunter; Soap; BWA; BFAST; BLAT; ZOOM; …
Main Fields: General and overarching topics; collections (00-XX); Combinatorics (05-XX); Number theory (11-XX)

STAR

Software Authors:   Alexander Dobin, Carrie A. Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R. Gingeras
Referenced in: 13 Publications (2015–2021)
Related Software: R; TopHat; edgeR; Bioconductor; Soap; Galaxy; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Numerical analysis (65-XX)

ABySS

Software Authors:   Simpson, J.T., Wong, K., Jackman, S.D., Schein, J.E., Jones, S.J., Birol, I.
Referenced in: 12 Publications (2012–2021)
Related Software: Velvet; SPAdes; SOAPdenovo; IDBA-UD; GAGE; ALLPATHS; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

iOri-Human

Software Authors:   Zhang, C.J.; Tang, H.; Li, W.C.
Referenced in: 13 Publications (2017–2022)
Related Software: iRNA-AI; pSuc-Lys; pLoc-mEuk; pLoc-mPlant; iPromoter-2L; iRSpot-EL; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

BSmooth

Software Authors:   Hansen, K., B. Langmead, R. Irizarry
Referenced in: 12 Publications (2016–2022)
Related Software: Bioconductor; MethylSig; Minfi; HMM-Fisher; HMM-DM; methylKit; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Computer science (68-XX)

TETRA

Software Authors:   Teeling H, Waldmann J, Lombardot T, Bauer M, Glöckner FO
Referenced in: 2 Publications (2011–2020)
Related Software: MEGAN; TACOA; BLAST; PSI-BLAST; DOTUR; Pfam; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

BEDTools

Software Authors:   Quinlan AR, Hall IM
Referenced in: 7 Publications (2012–2019)
Related Software: R; Soap; IGV; FastQC; Samtools; edgeR; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Computer science (68-XX)

GAGE

Software Authors:   Salzberg, S.L., Phillippy, A.M., Zimin, A., Puiu, D., Magoc, T., Koren, S., Treangen, T.J., Schatz, M.C., Delcher, A.L., Roberts, M., et al.
Referenced in: 10 Publications (2012–2019)
Related Software: Velvet; SPAdes; SOAPdenovo; ALLPATHS; ABySS; IDBA-UD; …
Main Fields: Combinatorics (05-XX); Probability theory and stochastic processes (60-XX); Statistics (62-XX)

Segmentor3IsBack

Software Authors:   Alice Cleynen, Michel Koskas, Emilie Lebarbier, Guillem Rigaill, Stephane Robin
Referenced in: 5 Publications (2017–2021)
Related Software: changepoint; wbs; R; FDRSeg; stepR; not; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX)

GenBank

Software Authors:   Dennis A. Benson; Mark Cavanaugh; Karen Clark; Ilene Karsch-Mizrachi; David J. Lipman; James Ostell; Eric W. Sayers
Referenced in: 5 Publications (2015–2020)
Related Software: LAGAN; MEGA; Surge; Staticman; Nix; Jekyll; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Numerical analysis (65-XX)

SHARCGS

Software Authors:   Dohm, J. C., Lottaz, C., Borodina, T.
Referenced in: 2 Publications (2012–2017)
Related Software: Velvet; ALLPATHS; SSAKE; BLAT; ARACHNE; QSRA; …
Main Fields: General and overarching topics; collections (00-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

SOPRA

Software Authors:   A. Dayarian, T.P. Michael, A.M. Sengupta
Referenced in: 7 Publications (2015–2021)
Related Software: GRASS; SCARPA; Bambus 2; BESST; Samtools; ScaffMatch; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

BS Seeker

Software Authors:   Chen, P. Y., S. J. Cokus, M. Pellegrini
Referenced in: 6 Publications (2012–2022)
Related Software: BSMAP; Bismark; BSmooth; Bowtie 2; SHRiMP; MethylCoder; …
Main Fields: General and overarching topics; collections (00-XX); Probability theory and stochastic processes (60-XX); Computer science (68-XX)

FindPeaks

Software Authors:   Fejes AP, Robertson G, Bilenky M, et al.
Referenced in: 3 Publications (2012–2013)
Related Software: BayesPeak; KEGG; DEGseq; edgeR; R; TileMap; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)

MaCH

Software Authors:   Li, Y., Willer, C. J., Ding, J., Scheet, P., Abecasis, G. R
Referenced in: 7 Publications (2013–2020)
Related Software: PLINK; R; pi-MASS; Matrix eQTL; MASS; MTAR; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Computer science (68-XX)

PhyloWGS

Software Authors:   Deshwar, A. G., Vembu, S., Yung, C. K., Jang, G. H., Stein, L., Morris, Q.
Referenced in: 7 Publications (2018–2021)
Related Software: PyClone; SciClone; TreeClone; R; PairClone; THetA; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Operations research, mathematical programming (90-XX)

SSAKE

Software Authors:   René L. Warren, Granger G. Sutton, Steven J. M. Jones, Robert A. Holt
Referenced in: 4 Publications (2015–2019)
Related Software: Velvet; SHARCGS; ABySS; IDBA-UD; SOAPdenovo; SPAdes; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

ZOOM

Software Authors:   Hao Lin, Zefeng Zhang, Michael Q. Zhang, Bin Ma, Ming Li
Referenced in: 5 Publications (2010–2018)
Related Software: Soap; SHRiMP; BWA; PatternHunter; CloudBurst; YASS; …
Main Fields: Combinatorics (05-XX); Number theory (11-XX); Computer science (68-XX)

BSMAP

Software Authors:   Xi, Y.; W. Li
Referenced in: 5 Publications (2012–2022)
Related Software: BS Seeker; Bismark; Bowtie 2; SHRiMP; Soap; mrsFAST; …
Main Fields: General and overarching topics; collections (00-XX); Probability theory and stochastic processes (60-XX); Computer science (68-XX)

CloudBurst

Software Authors:   Michael C. Schatz
Referenced in: 2 Publications (2013–2018)
Related Software: Soap; MrsRF; MapReduce; BWA; ZOOM; Crossbow; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

GOLD

Software Authors:   Reddy TBK, Thomas A, Stamatis D, Bertsch J, Isbandi M, Jansson J, Mallajosyula J, Pagani I, Lobos E, Kyrpides N
Referenced in: 4 Publications (2011–2017)
Related Software: miRBase; KEGG; MPRAP; BLAST; PSI-BLAST; PONDR-FIT; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Statistical mechanics, structure of matter (82-XX)

KMC

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

Quake

Software Authors:   D. R. Kelley, M. C. Schatz, S. L. Salzberg
Referenced in: 6 Publications (2011–2021)
Related Software: KmerStream; SHREC; Reptile; Fiona; HiTEC; ALLPATHS; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

SeqMap

Software Authors:   Jiang H, Wong WH
Referenced in: 3 Publications (2011–2015)
Related Software: ClustalW; DIALIGN; RAST; TopHat; SHRiMP; Clustal X; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Numerical analysis (65-XX)

Bismark

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

F-Seq

Software Authors:   –
Referenced in: 3 Publications (2011–2016)
Related Software: KEGG; Galaxy; ROAST; featureCounts; Rsubread; recount; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Biology and other natural sciences (92-XX)

featureCounts

Software Authors:   Liao Y, Smyth GK, Shi W
Referenced in: 5 Publications (2016–2018)
Related Software: R; edgeR; Bioconductor; BEDTools; MEDIPS; FastQC; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

GOtcha

Software Authors:   Martin, D.M., Berriman, M., Barton, G.J.
Referenced in: 3 Publications (2007–2008)
Related Software: GOPET; BayGO; Gaggle; GOLEM; BiNGO; ProbCD; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

GRASS

Software Authors:   A.A. Gritsenko, J.F. Nijkamp, M.J.T. Reinders, D. de Ridder
Referenced in: 5 Publications (2015–2021)
Related Software: SCARPA; SOPRA; Bambus 2; BESST; ScaffMatch; Velvet; …
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

methylKit

Software Authors:   Akalin, A., M. Kormaksson, S. Li, F. Garrett-Bakelman, M. Figueroa, A. Melnick, C. Mason
Referenced in: 5 Publications (2016–2021)
Related Software: HMM-Fisher; HMM-DM; BSmooth; Bioconductor; MOABS; Bisulfighter; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)

MethylSig

Software Authors:   Park, Y., M. E. Figueroa, L. S. Rozek, M. A. Sartor
Referenced in: 5 Publications (2016–2022)
Related Software: BSmooth; HMM-Fisher; MOABS; HMM-DM; Bisulfighter; methylKit; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)

ScaffMatch

Software Authors:   Mandric, I.; Zelikovsky, A.
Referenced in: 4 Publications (2016–2021)
Related Software: BESST; GRASS; Bambus 2; Velvet; SCARPA; SOPRA; …
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

WhatsHap

Software Authors:   Patterson M, Marschall T, Pisanti N, van Iersel L, Stougie L, Klau GW, Schönhuth A
Referenced in: 4 Publications (2017–2018)
Related Software: HapCol; QAPgrid; IgTree; Decombinator; SoDA2; Ab-origin; …
Main Fields: General and overarching topics; collections (00-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

ANNOVAR

Software Authors:   Wang K, Li M, Hakonarson H
Referenced in: 3 Publications (2014–2020)
Related Software: R; MEME; KEGG; WEKA; GenABEL; lme4; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Computer science (68-XX)

BESST

Software Authors:   Sahlin, K.; Vezzi, F.; Nystedt, B.; Lundeberg, J.; Arvestad, L.,
Referenced in: 4 Publications (2016–2021)
Related Software: GRASS; Bambus 2; ScaffMatch; Velvet; SCARPA; SOPRA; …
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

BFAST

Software Authors:   Homer, N., Merriman, B., Nelson, S.F.
Referenced in: 3 Publications (2010–2017)
Related Software: SHRiMP; PatternHunter; BWA; Soap; ART; GASSST; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

GenomeGraphs

Software Authors:   Durinck S, Bullard J.
Referenced in: 1 Publication (2016)
Related Software: Bioconductor; R; Rtracklayer; edgeR; Galaxy; ROAST; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

GenomicRanges

Software Authors:   P. Aboyoun, H. Pagès, M. Lawrence
Referenced in: 2 Publications (2014–2021)
Related Software: Bioconductor; R; ggplot2; GenomicAlignments; ASReml; IRanges; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

HMM-Fisher

Software Authors:   Sun, S., Yu, X.
Referenced in: 4 Publications (2016–2019)
Related Software: HMM-DM; BSmooth; methylKit; MOABS; Bisulfighter; MethylSig; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)

mGene

Software Authors:   Schweikert G, Zien A, Zeller G, Behr J, Dieterich C, Ong CS, Philips P, De Bona F, Hartmann L, Bohlen A
Referenced in: 3 Publications (2013–2017)
Related Software: LIBSVM; SplitsTree; MrBayes; Tracer; MulRF; iGTP; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Computer science (68-XX)

miRTarBase

Software Authors:   Chou CH, Chang NW, Shrestha S, Hsu SD, Lin YL, Lee WH, Yang CD, Hong HC, Wei TY, Tu SJ, Tsai TR, Ho SY, Jian TY, Wu HY, Chen PR, Lin NC, Huang HT, Yang TL, Pai CY, Tai CS, Chen WL, Huang CY, Liu CC, Weng SL, Liao KW, Hsu WL, Huang HD
Referenced in: 3 Publications (2013–2018)
Related Software: HIPPIE; STRING; DAVID; Algorithm 862; SylArray; Sylamer; …
Main Fields: Linear and multilinear algebra; matrix theory (15-XX); Statistics (62-XX); Operations research, mathematical programming (90-XX)

MOABS

Software Authors:   Sun, D., Y. Xi, B. Rodriguez, H. J. Park, P. Tong, M. Meong, M. A. Goodell, W. Li
Referenced in: 4 Publications (2016)
Related Software: Bioconductor; HMM-Fisher; HMM-DM; Bisulfighter; MethylSig; BSmooth; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)

MPSCAN

Software Authors:   E. Rivals, L. Salmela, P. Kiiskinen, P. Kalsi, J. Tarhio
Referenced in: 3 Publications (2010–2012)
Related Software: Iedera; PerM; PASS; BWA; ZOOM; PatMaN; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

Mugsy

Software Authors:   Samuel V. Angiuoli, Steven L. Salzberg
Referenced in: 3 Publications (2013–2017)
Related Software: MUSCLE; HMMER; MrBayes; iGTP; ProtTest 3; OXBench; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)

PerM

Software Authors:   Y. Chen, T. Souaiaia, T. Chen
Referenced in: 2 Publications (2010–2014)
Related Software: ZOOM; PatternHunter; SHRiMP; Iedera; MPSCAN; PASS; …
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

QUAST

Software Authors:   Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler
Referenced in: 4 Publications (2017–2019)
Related Software: Velvet; ABySS; SPAdes; Canu; Maligner; PBSIM; …
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

ReadDepth

Software Authors:   Miller, CA, et al.
Referenced in: 4 Publications (2015–2018)
Related Software: CNV-seq; R; ExomeWalker; BCFtools; HTQC; SNVer; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

SNVMix

Software Authors:   Goya, R. et al.
Referenced in: 3 Publications (2012–2018)
Related Software: VarScan; RSEM; STAR; edgeR; Sniper; GlfMultiples; …
Main Fields: General and overarching topics; collections (00-XX); Biology and other natural sciences (92-XX)

THetA

Software Authors:   Oesper, L., Mahmoody, A., Raphael, B. J.
Referenced in: 4 Publications (2015–2020)
Related Software: PyClone; R; PhyloWGS; BayCount; PairClone; TreeClone; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

BayCount

Software Authors:   Xie, Fangzheng; Zhou, Mingyuan; Xu, Yanxun
Referenced in: 3 Publications (2018–2021)
Related Software: R; PyClone; THetA; PhyloWGS; PairClone; TreeClone; …
Main Fields: Statistics (62-XX)

BEAT

Software Authors:   Akman, K., T. Haaf, S. Gravina, J. Vijg, A. Tresch
Referenced in: 3 Publications (2016–2017)
Related Software: BSmooth; methyAnalysis; HMM-Fisher; IMA; MOABS; HMM-DM; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)

Canu

Software Authors:   Sergey Koren, Brian P Walenz, Konstantin Berlin, Jason R Miller, Nicholas H Bergman, Adam M Phillippy
Referenced in: 3 Publications (2017–2019)
Related Software: SPAdes; CAMSA; hybridSPAdes; GTED; HINGE; Bandage; …
Main Fields: Biology and other natural sciences (92-XX)

CLIPZ

Software Authors:   Khorshid M, Rodak C, Zavolan M.
Referenced in: 2 Publications (2012–2014)
Related Software: HPeak; SpliceTrap; DWE; mirTools; miRExpress; TargetSpy; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)

csaw

Software Authors:   Lun, A. T. L., Smyth, G. K.
Referenced in: 3 Publications (2016–2018)
Related Software: limma; Bioconductor; diffHic; Voom; edgeR; DMRScan; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

deBGA

Software Authors:   B. Liu, H. Guo, M. Brudno, Y. Wang
Referenced in: 3 Publications (2017–2022)
Related Software: IDBA; BlastGraph; MEGAHIT; Velvet; IDBA-Tran; SplitMEM; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

Delly

Software Authors:   T. Rausch, T. Zichner, A. Schlattl, A. M. Stutz, V. Benes, J. O. Korbel
Referenced in: 2 Publications (2016–2017)
Related Software: Pindel; LUMPY; wgsim; Samtools; YAHA; GASV; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

HiTEC

Software Authors:   Ilie, L., Fazayeli, F., Ilie, S.
Referenced in: 2 Publications (2011–2017)
Related Software: SHREC; Reptile; Quake; ALLPATHS; BWA; Fiona; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

IGV

Software Authors:   Thorvaldsdóttir H, Robinson JT, Mesirov JP
Referenced in: 3 Publications (2016–2018)
Related Software: BEDTools; R; FastQC; Samtools; FIMO; BioMart; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)

IsoLasso

Software Authors:   Wei Li, Jianxing Feng, Tao Jiang
Referenced in: 2 Publications (2019–2022)
Related Software: Gurobi; MultiTrans; Scallop2; ShoRAH; SSP; StringTie; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

MaxBin

Software Authors:   Wu, Y.W., Simmons, B.A., Singer, S.W.
Referenced in: 3 Publications (2022)
Related Software: MetaBAT; GTDB-Tk; CheckM; MetaWRAP; MEGAHIT; GitHub; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

MetaGeneAnnotator

Software Authors:   Noguchi, H., Taniguchi, T., Itoh, T.
Referenced in: 1 Publication (2015)
Related Software: BLAST; PSI-BLAST; RePS; JBROWSE; ABySS; Artemis; …
Main Fields: Probability theory and stochastic processes (60-XX); Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

Oases

Software Authors:   Marcel H. Schulz, Daniel R. Zerbino, Martin Vingron, Ewan Birney
Referenced in: 3 Publications (2015–2017)
Related Software: SOAPdenovo; MetAMOS; Fiona; SPAdes; BLAT; Quake; …
Main Fields: General and overarching topics; collections (00-XX); Combinatorics (05-XX); Computer science (68-XX)

PBSIM

Software Authors:   Y. Ono, K. Asai, M. Hamada
Referenced in: 3 Publications (2017–2020)
Related Software: Canu; Maligner; OMBlast; ABySS; QUAST; Velvet; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

PCAP

Software Authors:   Huang, X., Wang, J., Aluru, S., Yang, S.P., Hillier, L.
Referenced in: 3 Publications (2007–2017)
Related Software: ClustalW; JBROWSE; InterProScan; MAKER; EasyGene; YACOP; …
Main Fields: General and overarching topics; collections (00-XX); Probability theory and stochastic processes (60-XX); Operations research, mathematical programming (90-XX)

PICS

Software Authors:   Zhang, Xuekui; Robertson, Gordon; Krzywinski, Martin; Ning, Kaida; Droit, Arnaud; Jones, Steven; Gottardo, Raphael
Referenced in: 3 Publications (2011–2015)
Related Software: nucleoSim; PuFFIN; nucleR; consensusSeekeR; VennDiagram; FindPeaks; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Biology and other natural sciences (92-XX)

ProSOM

Software Authors:   Thomas Abeel, Yvan Saeys, Pierre Rouze, Yves Van de Peer
Referenced in: 3 Publications (2009–2014)
Related Software: PromoterExplorer; BacPP; OligoPred; iLoc-Euk; iLoc-Hum; PseAAC-Builder; …
Main Fields: Harmonic analysis on Euclidean spaces (42-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

PurityEst

Software Authors:   Su, X., Zhang, L., Zhang, J., Meric-Bernstam, F. and Weinstein, J. N.
Referenced in: 3 Publications (2015–2021)
Related Software: BWA; PyClone; PurBayes; TreeClone; SciClone; PhyloWGS; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

RMBase

Software Authors:   Sun, W.-J.; Li, J.-H.; Liu, S.; Wu, J.; Zhou, H.; Qu, L.-H.; Yang, J.-H.
Referenced in: 3 Publications (2018–2019)
Related Software: iRNA-PseU; iRNAm5C-PseDNC; iRNA-PseColl; iRNA-3typeA; 2L-piRNA; iDNA6mA-PseKNC; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

rSW-seq

Software Authors:   T.M. Kim, L.J. Luquette, R. Xi, P.J. Park
Referenced in: 3 Publications (2016–2017)
Related Software: CNV-seq; SeqBBS; ReadDepth
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)

SnpEff

Software Authors:   Pablo Cingolani, Adrian Platts, Le Lily Wang, Melissa Coon, Tung Nguyen, Luan Wang, Susan J. Land, Xiangyi Lu, Douglas M. Ruden
Referenced in: 3 Publications (2016–2021)
Related Software: HTSeq; Samtools; Soap; STAR; R; Julia; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

SNVer

Software Authors:   Zhi Wei, Wei Wang, Pingzhao Hu, Gholson J. Lyon, Hakon Hakonarson
Referenced in: 3 Publications (2013–2018)
Related Software: Samtools; GATK; ExomeWalker; BCFtools; HTQC; Jannovar; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Biology and other natural sciences (92-XX)

SRA

Software Authors:   National Center for Biotechnology Information, U.S. National Library of Medicine
Referenced in: 3 Publications (2011–2014)
Related Software: EDAseq; changepoint; edgeR; Bioconductor; R; CRAN
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

Bambino

Software Authors:   . M.N. Edmonson, J. Zhang, C. Yan, R.P. Finney, D.M. Meerzaman, K.H. Buetow
Referenced in: 1 Publication (2014)
Related Software: UniProt; WebGestalt; KDDONTO; Protege; GeoSVM; GAMES; …
Main Fields: General and overarching topics; collections (00-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

bammds

Software Authors:   Malaspinas, A.-S.; Tange, O.; Moreno-Mayar, J. V.; Rasmussen, M.; DeGiorgio, M.; Wang, Y.; Valdiosera, C. E.; Politis, G.; Willerslev, E.; Nielsen, R.
Referenced in: 2 Publications (2016–2019)
Related Software: bmds; METAREP; mothur; PLINK
Main Fields: Statistics (62-XX); Game theory, economics, finance, and other social and behavioral sciences (91-XX); Biology and other natural sciences (92-XX)

BM-map

Software Authors:   Ji, Yuan; Xu, Yanxun; Zhang, Qiong; Tsui, Kam-Wah; Yuan, Yuan; Norris, Clift jun.; Liang, Shoudan; Liang, Han
Referenced in: 2 Publications (2011–2015)
Related Software: PyClone; BWA; PurityEst; PurBayes; Samtools; KEGG; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

CheckM

Software Authors:   Parks, DH; Imelfort, M.; Skennerton, CT; Hugenholtz, P.; Tyson, GW
Referenced in: 2 Publications (2022)
Related Software: GTDB-Tk; MetaWRAP; MaxBin; MetaBAT; MEGAHIT; CLMB; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

ConFunc

Software Authors:   Mark N. Wass, Michael J. E. Sternberg
Referenced in: 1 Publication (2010)
Related Software: ConSeq; PSLpred; iTOL; MAMMOTH; TM-align; BLAST; …
Main Fields: Biology and other natural sciences (92-XX)

CUSHAW

Software Authors:   Liu, Yongchao; Schmidt, Bertil
Referenced in: 2 Publications (2017)
Related Software: BWA; Bowtie 2; PatternHunter; SHRiMP; Soap; ART; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

CYNTENATOR

Software Authors:   Rödelsperger, C., Dieterich, C.
Referenced in: 2 Publications (2019)
Related Software: i-ADHoRe; CAMSA; hybridSPAdes; GTED; HINGE; Canu; …
Main Fields: General and overarching topics; collections (00-XX); Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

deBWT

Software Authors:   Liu, B.; Zhu, D.; Wang, Y.
Referenced in: 2 Publications (2017–2020)
Related Software:
Main Fields: Computer science (68-XX)

DMAP

Software Authors:   Stockwell, P. A., A. Chatterjee, E. J. Rodger. I. M. Morison
Referenced in: 2 Publications (2016)
Related Software: MethylSig; HMM-Fisher; COHCAP; SAAP-RRBS; MOABS; HMM-DM; …
Main Fields: Probability theory and stochastic processes (60-XX); Biology and other natural sciences (92-XX)

EMDUnifrac

Software Authors:   Jason McClelland, David Koslicki
Referenced in: 1 Publication (2018)
Related Software: ETE; Python; GitHub; EMD
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

ESTScan

Software Authors:   C. Iseli, C.V. Jongeneel, P. Bucher
Referenced in: 2 Publications (2007)
Related Software: ExonHunter; GlimmerHMM; TigrScan; EasyGene; Pfold
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Numerical analysis (65-XX)

ExaBayes

Software Authors:   Aberer AJ, Kobert K, Stamatakis A
Referenced in: 2 Publications (2017–2019)
Related Software: SplitsTree; MrBayes; MulRF; iGTP; Bio++; pIQPNNI; …
Main Fields: General and overarching topics; collections (00-XX); Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

FASTX

Software Authors:   Hannon laboratory
Referenced in: 2 Publications (2017–2018)
Related Software: VarScan; Trimmomatic; Samtools; GATK; MethylCoder; mrsFAST; …
Main Fields: Biology and other natural sciences (92-XX)

G-MAPSEQ

Software Authors:   Wojciechowski, Pawel; Frohmberg, Wojciech; Kierzynka, Michal; Zurkowski, Piotr; Blazewicz, Jacek
Referenced in: 2 Publications (2016–2020)
Related Software: Algorithm 457; R-CHIE; Bowtie 2; RazerS; Musket; G-DNA; …
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

GBSA

Software Authors:   Benoukraf, T.; Wongphayak, S.; Hadi, L. H.; Wu, M.; Soong, R.
Referenced in: 2 Publications (2016–2022)
Related Software: MethylSig; BSmooth; Minfi; fda (R); Bioconductor; Matlab
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

KmerStream

Software Authors:   Melsted, P., Halldórsson, B.V.
Referenced in: 2 Publications (2019–2021)
Related Software: Quake; Salmon; LBFGS-B; L-BFGS; L-BFGS-B; RNA-Skim; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

Lep-MAP

Software Authors:   Rastas P, Paulin L, Hanski I, Lehtonen R, Auvinen P
Referenced in: 0 Publications
Related Software: R; JoinMap; ICIMapping; onemap; MAPMAKER; qtl; …
Main Fields:

lobSTR

Software Authors:   Melissa Gymrek; David Golan; Saharon Rosset; Yaniv Erlich
Referenced in: 1 Publication (2016)
Related Software: PPS; Matlab
Main Fields: Harmonic analysis on Euclidean spaces (42-XX); Biology and other natural sciences (92-XX)

LUMPY

Software Authors:   Ryan M. Layer, Colby Chiang, Aaron R. Quinlan, Ira M. Hall
Referenced in: 1 Publication (2017)
Related Software: Pindel; Delly; wgsim; Samtools; YAHA; GASV; …
Main Fields: Biology and other natural sciences (92-XX)