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