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Found 376 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.
Cited in: 73 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)

DEseq

Software Authors:   Simon Anders
Cited in: 57 Publications (2011–2022)
Related Software: Bioconductor; edgeR; R; BaySeq; DESeq2; QuasiSeq; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Computer science (68-XX)

edgeR

Software Authors:   Mark D. Robinson; Davis J. McCarthy; Gordon K. Smyth
Cited in: 48 Publications (2011–2021)
Related Software: Bioconductor; R; DEseq; Voom; BaySeq; TopHat; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Numerical analysis (65-XX)

BioProspector

Software Authors:   Liu, X., Brutlag, D., Liu, J.
Cited 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
Cited 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)

Samtools

Software Authors:   Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R
Cited in: 16 Publications (2012–2019)
Related Software: BWA; Soap; GATK; R; VarScan; BLAT; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Computer science (68-XX)

BaySeq

Software Authors:   Thomas J Hardcastle; Krystyna A Kelly
Cited in: 16 Publications (2013–2018)
Related Software: Bioconductor; edgeR; DEseq; R; DESeq2; Voom; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Numerical analysis (65-XX)

GATK

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

MEGAN

Software Authors:   Daniel H. Huson, Alexander F. Auch, Ji Qi, Stephan C. Schuster
Cited in: 5 Publications (2010–2017)
Related Software: TETRA; TACOA; BLAST; ONE; RAST; PSI-BLAST; …
Main Fields: Combinatorics (05-XX); Statistics (62-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
Cited 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)

STAR

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

BEDTools

Software Authors:   Quinlan AR, Hall IM
Cited 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)

DEGseq

Software Authors:   Likun Wang; Zhixing Feng; Xi Wang; Xiaowo Wang; Xuegong Zhang
Cited in: 9 Publications (2012–2018)
Related Software: edgeR; Bioconductor; DEseq; R; BaySeq; Voom; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Numerical analysis (65-XX)

PoiClaClu

Software Authors:   Daniela Witten
Cited in: 10 Publications (2011–2022)
Related Software: R; penalizedLDA; rda; ElemStatLearn; edgeR; Bioconductor; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Computer science (68-XX)

Salmon

Software Authors:   Rob Patro, Geet Duggal, Michael I Love, Rafael A Irizarry, Carl Kingsford
Cited in: 9 Publications (2017–2022)
Related Software: HISAT; RSEM; edgeR; TopHat; StringTie; RNASeqReadSimulator; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

Segmentor3IsBack

Software Authors:   Alice Cleynen, Michel Koskas, Emilie Lebarbier, Guillem Rigaill, Stephane Robin
Cited 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)

FastQC

Software Authors:   Simon Andrews
Cited in: 7 Publications (2015–2021)
Related Software: R; TopHat; Trimmomatic; Bioconductor; STAR; KEGG; …
Main Fields: General and overarching topics; collections (00-XX); 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
Cited 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)

HTSeq

Software Authors:   Simon Anders, Paul Theodor Pyl, Wolfgang Huber
Cited in: 7 Publications (2016–2018)
Related Software: Bioconductor; edgeR; TopHat; STAR; R; DEseq; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

MAST

Software Authors:   Finak, G., McDavid, A., Yajima, M., Deng, J., Gersuk, V., Shalek, A. K., Slichter, C. K., Miller, H. W., McElrath, M. J., Prlic, M., Linsley, P. S., Gottardo, R.
Cited in: 8 Publications (2018–2021)
Related Software: ZIFA; CIDR; DEseq; DESeq2; KEGG; SC3; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

Minfi

Software Authors:   Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA
Cited in: 8 Publications (2016–2022)
Related Software: Bioconductor; BSmooth; MethylSig; IMA; limma; R; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)

Minimap2

Software Authors:   Li H
Cited in: 6 Publications (2019–2022)
Related Software: Winnowing; metaFlye; AMBER; Centrifuge; MaxBin; MetaBAT; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

Phyloseq

Software Authors:   Paul J. McMurdie; Susan Holmes
Cited in: 5 Publications (2015–2021)
Related Software: R; ggplot2; GUniFrac; shiny; vegan; multtest; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Biology and other natural sciences (92-XX)

RAST

Software Authors:   Meyer F, Paarmann D, D’Souza M et al
Cited in: 4 Publications (2012–2019)
Related Software: KEGG; MEGAN; Artemis; BLAST; PROSITE; PSI-BLAST; …
Main Fields: General and overarching topics; collections (00-XX); Probability theory and stochastic processes (60-XX); Computer science (68-XX)

SHARCGS

Software Authors:   Dohm, J. C., Lottaz, C., Borodina, T.
Cited in: 2 Publications (2012–2017)
Related Software: Velvet; ALLPATHS; SSAKE; ARACHNE; BLAT; 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
Cited 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)

VarScan

Software Authors:   Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK
Cited in: 7 Publications (2012–2019)
Related Software: Samtools; Trimmomatic; GATK; SNVMix; edgeR; mrsFAST; …
Main Fields: General and overarching topics; collections (00-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

BS Seeker

Software Authors:   Chen, P. Y., S. J. Cokus, M. Pellegrini
Cited 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.
Cited 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)

IDBA-UD

Software Authors:   Y. Peng, H.C. Leung, S.M. Yiu, F.Y. Chin
Cited in: 7 Publications (2015–2022)
Related Software: SPAdes; MEGAHIT; ABySS; SOAPdenovo; Velvet; IDBA; …
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

MaCH

Software Authors:   Li, Y., Willer, C. J., Ding, J., Scheet, P., Abecasis, G. R
Cited 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)

MultiCluster

Software Authors:   Wang, Miaoyan; Fischer, Jonathan; Song, Yun S.
Cited in: 7 Publications (2019–2022)
Related Software: CORALS; JIVE; MultiwayRegression; tensorregress; SupCP; TensorReg; …
Main Fields: Combinatorics (05-XX); Linear and multilinear algebra; matrix theory (15-XX); Statistics (62-XX)

PhyloWGS

Software Authors:   Deshwar, A. G., Vembu, S., Yung, C. K., Jang, G. H., Stein, L., Morris, Q.
Cited 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)

ART

Software Authors:   Weichun Huang, Leping Li, Jason R. Myers, Gabor T. Marth
Cited in: 6 Publications (2017–2022)
Related Software: BWA; Bowtie 2; ABySS; Velvet; hybridSPAdes; Vargas; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Computer science (68-XX)

BEAGLE

Software Authors:   Ayres, D.L., Darling, A., Zwickl, D.J., Beerli, P., Holder, M.T., Lewis, P.O., Huelsenbeck, J.P., Ronquist, F., Swofford, D.L., Cummings, M.P., Rambaut, A., Suchard, M.A.
Cited in: 4 Publications (2014–2022)
Related Software: R; BEAST; MrBayes; BEAUti; ape; Rcpp; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Numerical analysis (65-XX)

CloudBurst

Software Authors:   Michael C. Schatz
Cited 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
Cited 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
Cited 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)

mothur

Software Authors:   Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF.
Cited in: 4 Publications (2013–2021)
Related Software: pplacer; rtk; iNEXT; vegan; EstimateS; CURSAT; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Numerical analysis (65-XX)

SeqMap

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

ShortRead

Software Authors:   Martin Morgan, Simon Anders, Michael Lawrence, Patrick Aboyoun, Hervé Pagès, Robert Gentleman
Cited in: 2 Publications (2015–2021)
Related Software: Bioconductor; R; ggplot2; Rsamtools; TopHat; Trimmomatic; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

ShrinkBayes

Software Authors:   van de Wiel, M. A., Neerincx, M., Buffart, T. E., Sie, D., Verheul, H. M
Cited in: 6 Publications (2015–2021)
Related Software: Bioconductor; edgeR; BaySeq; DESeq2; Voom; R; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Biology and other natural sciences (92-XX)

sva

Software Authors:   Leek JT, Johnson WE, Parker HS, et al.
Cited in: 5 Publications (2016–2021)
Related Software: R; CRAN; systemPipeR; JASPAR; KEGG; Bioconductor; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

TopKLists

Software Authors:   Michael G. Schimek, Eva Budinska, Jie Ding, Karl G. Kugler, Vendula Svendova, Shili Lin
Cited in: 6 Publications (2015–2020)
Related Software: R; sets; relations; Rankcluster; Label.switching; PerMallows; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

Bismark

Software Authors:   Krueger, F.; S. Andrews
Cited 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)

casper

Software Authors:   Rossell, David; Attolini, Camille Stephan-Otto; Kroiss, Manuel; St"ocker, Almond
Cited in: 5 Publications (2014–2018)
Related Software: RSEM; TopHat; EBSeq; edgeR; Bioconductor; DRIMSeq; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)

d2_cluster

Software Authors:   Burke, J., Davison, D., Hide, W.
Cited in: 5 Publications (2007–2019)
Related Software: MOLPHY; PHYLIP; Rainbow; SlideSort; Mash; Corset; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Computer science (68-XX)

EDAseq

Software Authors:   Davide Risso; Sandrine Dudoit
Cited in: 5 Publications (2014–2018)
Related Software: DEseq; BaySeq; edgeR; Bioconductor; R; EXPANDER; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

F-Seq

Software Authors:   –
Cited 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)

GRASS

Software Authors:   A.A. Gritsenko, J.F. Nijkamp, M.J.T. Reinders, D. de Ridder
Cited 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)

IMP

Software Authors:   Peisen Zhang, Xiaolu Ye, Li Liao, James J. Russo, Stuart G. Fischer
Cited in: 5 Publications (2004–2020)
Related Software:
Main Fields: Combinatorics (05-XX); Computer science (68-XX)

methylKit

Software Authors:   Akalin, A., M. Kormaksson, S. Li, F. Garrett-Bakelman, M. Figueroa, A. Melnick, C. Mason
Cited in: 5 Publications (2016–2021)
Related Software: HMM-Fisher; HMM-DM; BSmooth; Bioconductor; MethylSig; MOABS; …
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
Cited in: 5 Publications (2016–2022)
Related Software: BSmooth; Minfi; Bioconductor; HMM-Fisher; MOABS; HMM-DM; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)

Mugsy

Software Authors:   Samuel V. Angiuoli, Steven L. Salzberg
Cited in: 4 Publications (2013–2022)
Related Software: MUSCLE; HMMER; Mauve; iGTP; MrBayes; ProtTest 3; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)

ScaffMatch

Software Authors:   Mandric, I.; Zelikovsky, A.
Cited 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)

slingshot

Software Authors:   Kelly Street, Davide Risso, Diya Das, Sandrine Dudoit, Koen Van den Berge, Robrecht Cannoodt
Cited in: 5 Publications (2008–2021)
Related Software: zinbwave; PMA; DESeq2; UMAP; ZIFA; Pyglrm; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Computer science (68-XX)

svaseq

Software Authors:   Jeffrey T. Leek
Cited in: 5 Publications (2015–2021)
Related Software: Bioconductor; R; DESeq2; DEseq; LBFGS-B; L-BFGS; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

Trimmomatic

Software Authors:   Anthony M. Bolger, Marc Lohse, Bjoern Usadel
Cited in: 4 Publications (2017–2021)
Related Software: FastQC; GATK; TopHat; R; VarScan; Samtools; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

ANNOVAR

Software Authors:   Wang K, Li M, Hakonarson H
Cited 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)

BFAST

Software Authors:   Homer, N., Merriman, B., Nelson, S.F.
Cited 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.
Cited 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
Cited 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)

GString

Software Authors:   H. Jiang, H. Wang, P.S. Yu, S. Zhou
Cited in: 3 Publications (2011–2016)
Related Software: Fg-index; GraphGrep; TALE; NeMa; GADDI; SAPPER; …
Main Fields: Computer science (68-XX); Operations research, mathematical programming (90-XX)

HMM-DM

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

HMM-Fisher

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

HPeak

Software Authors:   Qin ZS, Yu J, Shen J, et al.
Cited in: 4 Publications (2012–2016)
Related Software: BayesPeak; CLIPZ; COUNT; ARACHNE; SpliceTrap; DWE; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)

MetaSim

Software Authors:   Richter, D.C.; Ott, F.; Auch, A.F.; Schmid, R.; Huson, D.H.
Cited in: 2 Publications (2017–2018)
Related Software: ONE; BLAST; PSI-BLAST; MEGAN; Pfam; MetaCluster; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-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
Cited 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
Cited in: 4 Publications (2016)
Related Software: Bioconductor; MethylSig; HMM-Fisher; HMM-DM; Bisulfighter; BSmooth; …
Main Fields: Probability theory and stochastic processes (60-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)

PerM

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

ReadDepth

Software Authors:   Miller, CA, et al.
Cited 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)

SHREC

Software Authors:   Schroder, J., Schroder, H., Puglisi, S.J., Sinha, R., Schmidt, B.
Cited in: 3 Publications (2011–2018)
Related Software: Reptile; HiTEC; Quake; ALLPATHS; BWA; Fiona; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

SimSeq

Software Authors:   Samuel Benidt
Cited in: 3 Publications (2015–2019)
Related Software: R; edgeR; DEseq; Bioconductor; VCNet; ARACNE; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

Snakemake

Software Authors:   Köster, Johannes; Rahmann, Sven
Cited in: 0 Publications
Related Software: Taverna; Python; ImgLib2; scikit-image; CLIJ; CellProfiler; …
Main Fields:

SNVMix

Software Authors:   Goya, R. et al.
Cited 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.
Cited 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)

Bambus 2

Software Authors:   Koren, S., Treangen, T.J., Pop, M.
Cited in: 3 Publications (2016–2021)
Related Software: GRASS; SCARPA; SOPRA; BESST; ScaffMatch; Velvet; …
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

BamTools

Software Authors:   Barnett D. W., Garrison E. K., Quinlan A. R., Stromberg M. P., Marth G. T.
Cited in: 1 Publication (2019)
Related Software: BioClojure; BioRuby; LEVIATHAN; Samtools; LRez
Main Fields: Biology and other natural sciences (92-XX)

BayCount

Software Authors:   Xie, Fangzheng; Zhou, Mingyuan; Xu, Yanxun
Cited in: 3 Publications (2018–2021)
Related Software: R; PyClone; THetA; PhyloWGS; PairClone; TreeClone; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

BEAT

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

Bisulfighter

Software Authors:   Saito, Y., J. Tsuji, T. Mituyama
Cited in: 3 Publications (2016)
Related Software: MethylSig; HMM-Fisher; MOABS; HMM-DM; BSmooth; methylKit; …
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
Cited 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.
Cited in: 2 Publications (2012–2014)
Related Software: HPeak; ARACHNE; SpliceTrap; DWE; mirTools; miRExpress; …
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.
Cited 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
Cited in: 3 Publications (2017–2022)
Related Software: IDBA; DARRC; BlastGraph; MEGAHIT; Velvet; IDBA-Tran; …
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
Cited in: 2 Publications (2016–2017)
Related Software: Pindel; LUMPY; wgsim; Samtools; YAHA; GitHub; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

HiTEC

Software Authors:   Ilie, L., Fazayeli, F., Ilie, S.
Cited 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
Cited 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
Cited in: 2 Publications (2019–2022)
Related Software: HISAT; Salmon; Gurobi; MultiTrans; Scallop2; ShoRAH; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Operations research, mathematical programming (90-XX)

miRExpress

Software Authors:   Wang, W.C., Lin, F.M., Chang, W.C., Lin, K.Y., Huang, H.D., Lin, N.S.
Cited in: 2 Publications (2011–2012)
Related Software: ARACHNE; SpliceTrap; DWE; CLIPZ; mirTools; TargetSpy; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)

Oases

Software Authors:   Marcel H. Schulz, Daniel R. Zerbino, Martin Vingron, Ewan Birney
Cited 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)

PairClone

Software Authors:   Zhou, T., Müller, P., Sengupta, S., Ji, Y.
Cited in: 2 Publications (2019–2020)
Related Software: PyClone; TreeClone; PhyloWGS; THetA; BayCount; GitHub; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

PCAP

Software Authors:   Huang, X., Wang, J., Aluru, S., Yang, S.P., Hillier, L.
Cited in: 3 Publications (2007–2017)
Related Software: ClustalW; PHYLIP; JBROWSE; InterProScan; MAKER; EasyGene; …
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
Cited 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)

Prokka

Software Authors:   Torsten Seemann
Cited in: 1 Publication (2016)
Related Software: HMMER; MAFFT; eggNOG; R; Gubbins; SeqKit; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

PurityEst

Software Authors:   Su, X., Zhang, L., Zhang, J., Meric-Bernstam, F. and Weinstein, J. N.
Cited 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)

RAPSearch2

Software Authors:   Zhao Y, Tang H, Ye Y
Cited in: 2 Publications (2017–2019)
Related Software: PHYLIP; Tracer; MulRF; iGTP; TOPAL; ExaBayes; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)