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Found 56 Software Packages (Results 1–56)

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)

ZIFA

Software Authors:   Pierson, E.; Yau, C.
Cited in: 13 Publications (2018–2021)
Related Software: CIDR; t-SNE; MAST; SNN-Cliq; zinbwave; DESeq2; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Computer science (68-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)

SC3

Software Authors:   Vladimir Yu Kiselev, Kristina Kirschner, Michael T. Schaub, Tallulah Andrews, Andrew Yiu, Tamir Chandra, Kedar N. Natarajan, Wolf Reik, Mauricio Barahona, Anthony R Green, Martin Hemberg
Cited in: 8 Publications (2017–2021)
Related Software: CIDR; ZIFA; SNN-Cliq; DESeq2; MAST; DEseq; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

CIDR

Software Authors:   Lin, P., Troup, M., Ho, J. W. K.
Cited in: 7 Publications (2018–2021)
Related Software: ZIFA; MAST; SC3; SNN-Cliq; DESeq2; DEseq; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

AgentCell

Software Authors:   Thierry Emonet, Charles M. Macal, Michael J. North, Charles E. Wickersham, Philippe Cluzel
Cited in: 6 Publications (2007–2020)
Related Software: BacSim; FreeFem++; STOCHSIM
Main Fields: Partial differential equations (35-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)

SNN-Cliq

Software Authors:   Chen Xu; Zhengchang Su
Cited in: 6 Publications (2017–2021)
Related Software: ZIFA; CIDR; SC3; MAST; mixtools; GlobalMIT; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

zinbwave

Software Authors:   Davide Risso, Svetlana Gribkova, Fanny Perraudeau, Jean-Philippe Vert, Clara Bagatin
Cited in: 6 Publications (2008–2021)
Related Software: ZIFA; DESeq2; t-SNE; DEseq; Bioconductor; slingshot; …
Main Fields: Statistics (62-XX); Numerical analysis (65-XX); Biology and other natural sciences (92-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)

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: Statistics (62-XX); Biology and other natural sciences (92-XX)

SPhyR

Software Authors:   Mohammed El-Kebir
Cited in: 3 Publications (2020–2021)
Related Software: SCARLET; BEAST; bioperl; SackinMinimizer; Mathematica
Main Fields: Combinatorics (05-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

BPSC

Software Authors:   T. N. Vu, Q. F. Wills, K. R. Kalari, N. Niu, L. Wang, M. Rantalainen, Y. Pawitan
Cited in: 2 Publications (2018–2021)
Related Software: SimBPDD; splatter; R; ZIFA; CIDR; MAST; …
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
Cited in: 2 Publications (2022)
Related Software: GTDB-Tk; MetaWRAP; MaxBin; MetaBAT; MEGAHIT; BWA; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

DIMM-SC

Software Authors:   Sun, Z., Wang, T., Deng, K., XF, W., Lafyatis, R., Ding, Y. et al.
Cited in: 2 Publications (2020–2022)
Related Software: umap; pcaReduce; DESeq2; SNN-Cliq; ZIFA; CIDR; …
Main Fields: Statistics (62-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; GeneNetWeaver; Path2Models; SOSlib; LASSIE; BioPreDyn-bench; …
Main Fields: Biology and other natural sciences (92-XX)

Noise2Self

Software Authors:   Joshua Batson, Loic Royer
Cited in: 1 Publication (2022)
Related Software: bmiptools; Scikit; Amira; Fiji; Dragonfly; OpenCV; …
Main Fields: Statistics (62-XX)

OpenCarp

Software Authors:   Plank, G., Loewe, A., Neic, A., Augustin, C., Huang, Y.-L., Gsell, M. A., Karabelas, E., Nothstein, M., Prassl, A. J., Sánchez, J., et al
Cited in: 1 Publication (2022)
Related Software: FEniCS; GEMS; pulse; simcardems; Chaste; SimVascular; …
Main Fields: Mechanics of deformable solids (74-XX); Biology and other natural sciences (92-XX)

pcaReduce

Software Authors:   Justina Zurauskiene. Christopher Yau
Cited in: 2 Publications (2017–2022)
Related Software: DIMM-SC; umap; pdfCluster; PRMLT; Sincera; SC3; …
Main Fields: Statistics (62-XX); Computer science (68-XX)

SCARLET

Software Authors:   Satas, G., Zaccaria, S., Mon, G., Raphael, B. J.
Cited in: 2 Publications (2021–2022)
Related Software: TreeMHN; pathTiMEx; BiTSC2; SiFit; SPhyR
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

scater

Software Authors:   McCarthy DJ, Campbell KR, Lun ATL, Willis QF
Cited in: 2 Publications (2019–2022)
Related Software: t-SNE; knitr; scRNAseq; tourr; R; CIDR; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

SEQuel

Software Authors:   Roy Ronen, Christina Boucher, Hamidreza Chitsaz, Pavel Pevzner
Cited in: 2 Publications (2016–2017)
Related Software: SPAdes; Canu; Maligner; PBSIM; OMBlast; ABySS; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

SiFit

Software Authors:   Hamim Zafar, Anthony Tzen, Nicholas Navin, Ken Chen, Luay Nakhleh
Cited in: 1 Publication (2022)
Related Software: TreeMHN; pathTiMEx; BiTSC2; SCARLET; BitPhylogeny; PhyloWS
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

Sincera

Software Authors:   Minzhe Guo, Hui Wang, S Steven Potter, Jeffrey A Whitsett, Yan Xu
Cited in: 2 Publications (2017–2021)
Related Software: SC3; GlobalMIT; slingshot; SNN-Cliq; MrTADFinder; CIDR; …
Main Fields: Statistics (62-XX); Computer science (68-XX)

splatter

Software Authors:   Luke Zappia, Belinda Phipson, Alicia Oshlack
Cited in: 1 Publication (2021)
Related Software: R; Matrix; GeneNetWeaver; Voom; mvtnorm; igraph; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

adaSC3

Software Authors:   Fuetterer, Cornelia; Augustin, Thomas; Fuchs, Christiane
Cited in: 1 Publication (2020)
Related Software: lle; destiny; SC3; emdbook; Scikit; vegan; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

BayICE

Software Authors:   Tai, An-Shun; Tseng, George C.; Hsieh, Wen-Ping
Cited in: 1 Publication (2021)
Related Software: ISOpureR; dtangle; BayCount; spikeslab; R
Main Fields: Statistics (62-XX)

BiTSC2

Software Authors:   Ziwei Chen, Fuzhou Gong, Lin Wan, Liang Ma
Cited in: 1 Publication (2022)
Related Software: TreeMHN; pathTiMEx; SCARLET; SiFit
Main Fields: Biology and other natural sciences (92-XX)

BLGGM

Software Authors:   Wu, Qiuyu; Luo, Xiangyu
Cited in: 1 Publication (2022)
Related Software: igraph; BDgraph; HeteroGGM; PLNseq; R
Main Fields: Statistics (62-XX)

cisTopic

Software Authors:   González-Blas CB, et al.
Cited in: 0 Publications
Related Software: GibbsLDA++; StanfordCoreNLP; topicmodels; TopicModel4J
Main Fields:

clusterExperiment

Software Authors:   Elizabeth Purdom, Davide Risso
Cited in: 1 Publication (2008)
Related Software: slingshot; seqLogo; scone; Genominator; affxparser; marray; …
Main Fields: Statistics (62-XX)

CytoBackBone

Software Authors:   Leite Pereira, A.; Lambotte, O.; Le Grand, R.; Cosma, A.; Tchitchek, N.
Cited in: 1 Publication (2022)
Related Software: CyTOFmerge; RecordLinkage; transport; MICE; sn
Main Fields: Statistics (62-XX)

CyTOFmerge

Software Authors:   Abdelaal, T.; Höllt, T.; van Unen, V.; Lelieveldt, B. P.F.; Koning, F.; Reinders, M. J.T.; Mahfouz, A.
Cited in: 1 Publication (2022)
Related Software: CytoBackBone; RecordLinkage; transport; MICE; sn
Main Fields: Statistics (62-XX)

DeepCyTOF

Software Authors:   H. Li, U. Shaham, K. Stanton, Y. Yao, R. Montgomery, Y. Kluger
Cited in: 0 Publications
Related Software: mclust; flowLearn; flowClust; flowPeaks; Tclust; Bioconductor; …
Main Fields:

DropLasso

Software Authors:   Khalfaoui, B., Vert, J.P.
Cited in: 1 Publication (2022)
Related Software: HieRFIT; seagull; msgl; biglasso; AS 136; R
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

glmGamPoi

Software Authors:   Ahlmann-Eltze, C.; Huber, W.
Cited in: 1 Publication (2021)
Related Software: FLUPS; ppmlhdfe
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

HieRFIT

Software Authors:   Kaymaz, Y., Ganglberger, F., Tang, M., Fernandez-Albert, F., Lawless, N., Sackton, T.B
Cited in: 1 Publication (2022)
Related Software: DropLasso; seagull; msgl; biglasso; AS 136; R
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

MEMO

Software Authors:   Geissen, E.-M., J. Hasenauer, S. Heinrich, S. Hauf, F. J. Theis, N. E. Radde
Cited in: 1 Publication (2019)
Related Software: PRMLT; PMTK; flowClust; mixtools
Main Fields: Statistics (62-XX)

powsimR

Software Authors:   B. Vieth, C. Ziegenhain, S. Parekh, W. Enard, I. Hellmann
Cited in: 1 Publication (2020)
Related Software: zinbwave; ZIFA; MAST; DEseq
Main Fields: Biology and other natural sciences (92-XX)

Scallop2

Software Authors:   Qimin Zhang, Qian Shi, Mingfu Shao
Cited in: 1 Publication (2022)
Related Software: HISAT; Salmon; Gurobi; MultiTrans; ShoRAH; SSP; …
Main Fields: Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

scModels

Software Authors:   Lisa Amrhein, Kumar Harsha, Christiane Fuchs, Pavel Holoborodko
Cited in: 1 Publication (2021)
Related Software: curatedOvarianData; dynpred; joint.Cox
Main Fields: Statistics (62-XX)

scone

Software Authors:   Michael Cole, Davide Risso
Cited in: 1 Publication (2008)
Related Software: slingshot; seqLogo; Genominator; clusterExperiment; affxparser; marray; …
Main Fields: Statistics (62-XX)

scran

Software Authors:   Aaron Lun, Karsten Bach
Cited in: 0 Publications
Related Software: igraph; Bioconductor; SIMLR
Main Fields:

SHARP

Software Authors:   Wan, S.; Kim, J.; Won, KJ
Cited in: 1 Publication (2022)
Related Software: RSpectra; PASTA; UMAP; idm; onlinePCA; irlba; …
Main Fields: Numerical analysis (65-XX)

sicegar

Software Authors:   M. Umut Caglar, Claus O. Wilke
Cited in: 1 Publication (2021)
Related Software:
Main Fields: Game theory, economics, finance, and other social and behavioral sciences (91-XX)

SimBPDD

Software Authors:   Schefzik, Roman
Cited in: 1 Publication (2021)
Related Software: BPSC; splatter; R
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

SIMLR

Software Authors:   Bo Wang, Daniele Ramazzotti, Luca De Sano, Junjie Zhu, Emma Pierson, Serafim Batzoglou
Cited in: 0 Publications
Related Software: scran; igraph; Bioconductor
Main Fields:

SingleCellExperiment

Software Authors:   Aaron Lun, Davide Risso, Keegan Korthauer, Kevin Rue-Albrecht
Cited in: 0 Publications
Related Software: BiocParallel; t-SNE; Bioconductor; R; scPCA
Main Fields:

SPRING

Software Authors:   Caleb Weinreb, Samuel Wolock, Allon M Klein
Cited in: 1 Publication (2019)
Related Software:
Main Fields: Biology and other natural sciences (92-XX)

SSLB

Software Authors:   Moran, Gemma E.; Ročková, Veronika; George, Edward I.
Cited in: 1 Publication (2021)
Related Software: clusterProfiler; breastCancerNKI; FABIA; GitHub; COSA; LAS
Main Fields: Statistics (62-XX)

TRONCO

Software Authors:   Luca De Sano, Giulio Caravagna, Daniele Ramazzotti, Alex Graudenzi, Giancarlo Mauri, Bud Mishra, Marco Antoniotti
Cited in: 0 Publications
Related Software: Bioconductor
Main Fields:

Usiigaci

Software Authors:   Hsieh-Fu Tsai, Joanna Gajda, Tyler F.W. Sloan, Andrei Rares, Jason Ting-Chun Chou, Amy Q. Shen
Cited in: 0 Publications
Related Software: PyQt; Seaborn; Matplotlib; scikit-image; FogBank; CUDA; …
Main Fields:

WemIQ

Software Authors:   Zhang, J., Kuo, C.-C. J., Chen, L.
Cited in: 1 Publication (2018)
Related Software: CLIIQ; MITIE; GENCODE; RSEM; TopHat; casper
Main Fields: Statistics (62-XX)

Bignorm

Software Authors:   Axel Wedemeyer, Lasse Kliemann, Anand Srivastav, Christian Schielke, Thorsten B. Reusch, Philip Rosenstiel
Cited in: 0 Publications
Related Software:
Main Fields:

DeLorean

Software Authors:   John Reid
Cited in: 0 Publications
Related Software:
Main Fields:

noise

Software Authors:   Audrey Qiuyan Fu; Lior Pachter
Cited in: 0 Publications
Related Software:
Main Fields: