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Found 132 Software Packages (Results 1–100)

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)

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)

Voom

Software Authors:   Law, C. W., Chen, Y., Shi, W., Smyth, G. K.
Referenced in: 18 Publications (2015–2021)
Related Software: edgeR; Bioconductor; R; limma; DEseq; DESeq2; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-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; FastQC; …
Main Fields: Combinatorics (05-XX); Statistics (62-XX); Numerical analysis (65-XX)

ZIFA

Software Authors:   Pierson, E.; Yau, C.
Referenced 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)

RSEM

Software Authors:   Li B, Dewey CN
Referenced in: 12 Publications (2015–2021)
Related Software: edgeR; Bioconductor; TopHat; R; DEseq; Salmon; …
Main Fields: General and overarching topics; collections (00-XX); Probability theory and stochastic processes (60-XX); Statistics (62-XX)

DEGseq

Software Authors:   Likun Wang; Zhixing Feng; Xi Wang; Xiaowo Wang; Xuegong Zhang
Referenced 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)

recount

Software Authors:   Leonardo Collado-Torres, Abhinav Nellore, Andrew E. Jaffe, Margaret A. Taub, Kai Kammers, Shannon E. Ellis, Kasper Daniel Hansen, Ben Langmead, Jeffrey T. Leek
Referenced in: 9 Publications (2014–2019)
Related Software: edgeR; Bioconductor; R; BaySeq; CAPUSHE; DESeq2; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

Salmon

Software Authors:   Rob Patro, Geet Duggal, Michael I Love, Rafael A Irizarry, Carl Kingsford
Referenced in: 9 Publications (2017–2022)
Related Software: RSEM; edgeR; TopHat; StringTie; RNASeqReadSimulator; iClusterPlus; …
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
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)

EBSeq

Software Authors:   Leng N, Dawson JA, Thomson JA, Ruotti V, Rissman AI, Smits BM, Haag JD, Gould MN, Stewart RM, Kendziorski C
Referenced in: 8 Publications (2015–2021)
Related Software: edgeR; Bioconductor; DEseq; TopHat; BaySeq; DESeq2; …
Main Fields: General and overarching topics; collections (00-XX); Probability theory and stochastic processes (60-XX); Statistics (62-XX)

HTSeq

Software Authors:   Simon Anders, Paul Theodor Pyl, Wolfgang Huber
Referenced 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)

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
Referenced 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.
Referenced 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)

MultiCluster

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

QuasiSeq

Software Authors:   Steve Lund; Long Qu
Referenced in: 7 Publications (2012–2018)
Related Software: DEseq; Bioconductor; Voom; edgeR; limma; BaySeq; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

HISAT

Software Authors:   D. Kim, B. Langmead, S. L. Salzberg
Referenced in: 4 Publications (2017–2021)
Related Software: STAR; TopHat; edgeR; R; Bowtie 2; KEGG; …
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)

MapSplice

Software Authors:   Wang, Darshan Singh, Zheng Zeng, Stephen J. Coleman, Yan Huang,Gleb L. Savich, Xiaping He, Piotr Mieczkowski, Sara A. Grimm, Charles M.Perou, James N. MacLeod, Derek Y. Chiang, Jan F. Prins, Jinze Liu
Referenced in: 6 Publications (2016–2019)
Related Software: STAR; RSEM; BWA; Soap; TopHat; R; …
Main Fields: Statistics (62-XX); Computer science (68-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
Referenced 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)

zinbwave

Software Authors:   Davide Risso, Svetlana Gribkova, Fanny Perraudeau, Jean-Philippe Vert, Clara Bagatin
Referenced 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)

casper

Software Authors:   Rossell, David; Attolini, Camille Stephan-Otto; Kroiss, Manuel; St"ocker, Almond
Referenced 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)

EDAseq

Software Authors:   Davide Risso; Sandrine Dudoit
Referenced 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)

RUVseq

Software Authors:   Davide Risso; Sandrine Dudoit
Referenced in: 5 Publications (2014–2019)
Related Software: DEseq; BaySeq; Bioconductor; Voom; DEGseq; edgeR; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

GenePattern

Software Authors:   Michael Reich, Ted Liefeld, Joshua Gould, Jim Lerner, Pablo Tamayo, Jill P Mesirov
Referenced in: 1 Publication (2016)
Related Software: R; PlantTFDB; eggNOG; ELM; dbCAN; antiSMASH; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

GPSeq

Software Authors:   Srivastava, S.; L. Chen
Referenced in: 4 Publications (2014–2019)
Related Software: DEseq; R; BayesDA; ePCA; GitHub; PMA; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

GSVA

Software Authors:   Hänzelmann S, Castelo R, Guinney J
Referenced in: 4 Publications (2014–2021)
Related Software: Bioconductor; MSigDB; ROAST; DAVID; KEGG; edgeR; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

SimSeq

Software Authors:   Samuel Benidt
Referenced 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)

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)

CIDANE

Software Authors:   Stefan Canzar, Sandro Andreotti, David Weese, Knut Reinert, Gunnar W Klau
Referenced in: 2 Publications (2020–2022)
Related Software: Gurobi; MultiTrans; Scallop2; ShoRAH; SSP; StringTie; …
Main Fields: Computer science (68-XX); Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

CLIIQ

Software Authors:   Lin, Y.-Y., Dao, P., Hach, F., Bakhshi, M., Mo, F., Lapuk, A., Collins, C., Sahinalp, S. C.
Referenced in: 2 Publications (2018–2022)
Related Software: Gurobi; MultiTrans; Scallop2; ShoRAH; SSP; StringTie; …
Main Fields: Statistics (62-XX); Operations research, mathematical programming (90-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)

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)

onechannelgui

Software Authors:   Sanges R, Cordero F, Calogero RA
Referenced in: 1 Publication (2015)
Related Software: Bioconductor; EMIRGE; ViennaRNA; TagCleaner; OligoWalk; OptiRNAi; …
Main Fields: General and overarching topics; collections (00-XX); Biology and other natural sciences (92-XX)

RNASeqReadSimulator

Software Authors:   Wei Li
Referenced in: 3 Publications (2017–2022)
Related Software: StringTie; Salmon; Gurobi; MultiTrans; Scallop2; ShoRAH; …
Main Fields: Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-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
Referenced 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)

SCODE

Software Authors:   Matsumoto H, Kiryu H, Furusawa C, Ko MSH, Ko SBH, Gouda N, Hayashi T, Nikaido I
Referenced in: 3 Publications (2019–2021)
Related Software: SCENIC; glasso; DINGO; ARACNE; KEGG; WGCNA; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

SpliceTrap

Software Authors:   Wu J, Akerman M, et al.
Referenced in: 3 Publications (2012–2016)
Related Software: TopHat; edgeR; R; BaySeq; rSeqDiff; MOABS; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)

systemPipeR

Software Authors:   Backman, T.W.H; Girke, T.
Referenced in: 2 Publications (2019–2021)
Related Software: KEGG; R; STAR; TopHat; FactoMineR; ggplot2; …
Main Fields: Statistics (62-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)

BPSC

Software Authors:   T. N. Vu, Q. F. Wills, K. R. Kalari, N. Niu, L. Wang, M. Rantalainen, Y. Pawitan
Referenced 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)

CountClust

Software Authors:   Dey K, Hsiao C, Stephens M
Referenced in: 2 Publications (2019–2021)
Related Software: fastTopics; GitHub; MultiCluster; GeneCards; t-SNE; SigClust; …
Main Fields: Linear and multilinear algebra; matrix theory (15-XX); Statistics (62-XX); Numerical analysis (65-XX)

DEXUS

Software Authors:   Klambauer G, Unterthiner T, Hochreiter S.
Referenced in: 2 Publications (2016–2017)
Related Software: missForest; recount; HTSeq; impute; VIM; STAR; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

ExpEdit

Software Authors:   Picardi E, D’Antonio M, Carrabino D, Castrignanò T, Pesole G.
Referenced in: 1 Publication (2015)
Related Software: EMIRGE; ViennaRNA; TagCleaner; OligoWalk; OptiRNAi; ASTALAVISTA; …
Main Fields: General and overarching topics; collections (00-XX); Biology and other natural sciences (92-XX)

gage

Software Authors:   Weijun Luo
Referenced in: 2 Publications (2016–2021)
Related Software: edgeR; Bioconductor; STAR; intePareto; iClusterPlus; BiSeq; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-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)

GENCODE

Software Authors:   Harrow J, Frankish A, Gonzalez JM et al
Referenced in: 2 Publications (2017–2018)
Related Software: CLIIQ; MITIE; WemIQ; RSEM; TopHat; casper; …
Main Fields: General and overarching topics; collections (00-XX); Statistics (62-XX); Biology and other natural sciences (92-XX)

PLNseq

Software Authors:   Zhang, H.; Xu, J.; Jiang, N.; Hu, X.; Luo, Z.
Referenced in: 2 Publications (2020–2022)
Related Software: R; HeteroGGM; BLGGM; BDgraph; igraph; maSigPro; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

PROPER

Software Authors:   Hao Wu
Referenced in: 2 Publications (2016)
Related Software: Bioconductor; GENE-counter; Scotty; DEseq; DEGseq; SAS; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

RSeQC

Software Authors:   Wang L, Wang S, Li W
Referenced in: 1 Publication (2015)
Related Software: BUSCO; TRINITY; Bowtie 2; Python; GUESSmyLT; EMIRGE; …
Main Fields: General and overarching topics; collections (00-XX); Biology and other natural sciences (92-XX)

rSeqDiff

Software Authors:   Shi, Y.; Jiang, H.
Referenced in: 2 Publications (2016–2018)
Related Software: EBSeq; TopHat; BaySeq; edgeR; Bioconductor; DESeq2; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

scater

Software Authors:   McCarthy DJ, Campbell KR, Lun ATL, Willis QF
Referenced 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)

scRNAseq

Software Authors:   Risso, D.; Cole, M.
Referenced in: 2 Publications (2019–2022)
Related Software: t-SNE; knitr; scater; tourr; R; SNN-Cliq; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

Sincera

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

StringTie

Software Authors:   Pertea, M., Pertea, G.M., Antonescu, C.M., Chang, T.C., Mendell, J.T., Salzberg, S.L.
Referenced in: 2 Publications (2022)
Related Software: RNASeqReadSimulator; Salmon; Gurobi; MultiTrans; Scallop2; ShoRAH; …
Main Fields: Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

abSNP

Software Authors:   Mao, Shunfu; Mohajer, Soheil; Ramachandran, Kannan; Tse, David; Kannan, Sreeram
Referenced in: 1 Publication (2017)
Related Software: Sniper; GlfMultiples; RNASeqReadSimulator; SNVMix; VarScan; RSEM; …
Main Fields: Biology and other natural sciences (92-XX)

AC-PCA

Software Authors:   Z. Lin, C. Yang, Y. Zhu, J. C. Duchi, Y. Fu, Y. Wang, B. Jiang, M. Zamanighomi, X. Xu, M. Li, N. Sestan, H. Zhao, W. H. Wong
Referenced in: 1 Publication (2016)
Related Software: Matlab; GitHub; R
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

AugmentedPCA

Software Authors:   William E. Carson IV, Austin Talbot, David Carlson
Referenced in: 0 Publications
Related Software: SciPy; UMAP; NumPy; Scikit; Python
Main Fields:

BayICE

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

BCDForest

Software Authors:   Yang Guo, Shuhui Liu, Zhanhuai Li, Xuequn Shang
Referenced in: 1 Publication (2020)
Related Software: boost; rL-GenSVM; SGL-SVM; GitHub; ROCR
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

Bioinformatics Toolbox

Software Authors:   mathworks
Referenced in: 0 Publications
Related Software: panp; RcppGSL; Ox; Affymetrix; Matlab; Bioconductor; …
Main Fields:

compcodeR

Software Authors:   Charlotte Soneson
Referenced in: 1 Publication (2016)
Related Software: BaySeq; DESeq2; DEXUS; Voom; QuasiSeq; DEseq; …
Main Fields: Statistics (62-XX)

contamDE

Software Authors:   Shen Q, Hu J, Jiang N, Hu X, Luo Z, Zhang H
Referenced in: 1 Publication (2019)
Related Software: Accurity; UNDO; MethylPurify; InfiniumPurify; QUBIC; THetA; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

Cox-nnet

Software Authors:   Ching, T.; Zhu, X.; Garmire, LX
Referenced in: 1 Publication (2021)
Related Software: DeepSurv; Albatross Analytics; crrSC; dhglm; frailtyHL; cmprsk; …
Main Fields: Statistics (62-XX)

deFuse

Software Authors:   McPherson, Hormozdiari, Zayed, et al.
Referenced in: 1 Publication (2021)
Related Software: STAR; intePareto; iClusterPlus; BiSeq; MethylSeekR; rGREAT; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

DiffSplice

Software Authors:   Hu, Y., Huang, Y., Du, Y., Orellana, C. F., Singh, D., Johnson, A. R., Monroy, A., Kuan, P. F., Hammond, S. M., Makowski, L., Randell, S. H., Chiang, D. Y., Hayes, D. N., Jones, C., Liu, Y., Prins, J. F., Liu, J.
Referenced in: 1 Publication (2016)
Related Software: BaySeq; SpliceTrap; rSeqDiff; MOABS; EBSeq; TopHat; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

DoubleExpSeq

Software Authors:   Sean Ruddy
Referenced in: 1 Publication (2016)
Related Software: BaySeq; SpliceTrap; rSeqDiff; MOABS; EBSeq; TopHat; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

DRIMSeq

Software Authors:   Nowicka, M.; M. Robinson
Referenced in: 1 Publication (2017)
Related Software: EBSeq; RSEM; TopHat; HTSeq; LaplacesDemon; limma; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

DropLasso

Software Authors:   Khalfaoui, B., Vert, J.P.
Referenced 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)

EmpDiff

Software Authors:   Thorne, Thomas
Referenced in: 1 Publication (2015)
Related Software: DESeq2; SimSeq; recount; EBSeq; KEGG; DEseq; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

eSNV-detect

Software Authors:   Tang, Xiaojia; Baheti, Saurabh; Kalari, Krishna R.
Referenced in: 1 Publication (2018)
Related Software: HaploReg; MapSplice; Strelka; Salmon; ZOOM; SomaticSniper; …
Main Fields: Biology and other natural sciences (92-XX)

FSCseq

Software Authors:   Lim, D. K., Rashid, N. U., Ibrahim, J. G
Referenced in: 1 Publication (2021)
Related Software: DESeq2; NB.MClust; iClusterPlus; zinbwave; TCGAbiolinks; Salmon; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

FStitch

Software Authors:   Azofeifa J, Allen MA, Lladser ME, Dowell R
Referenced in: 1 Publication (2017)
Related Software: Vespucci
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

FX

Software Authors:   D. Hong, A. Rhie, S.-S. Park et al.
Referenced in: 1 Publication (2013)
Related Software: Crossbow; Probalign; k-means++; Jnomics; T-coffee; Kalign; …
Main Fields: Biology and other natural sciences (92-XX)

GENE-counter

Software Authors:   Cumbie, J. S., J. A. Kimbrel, Y. Di, D. W. Schafer, L. J. Wilhelm, S. E. Fox, C. M. Sullivan, A. D. Curzon, J. C. Carrington, T. C. Mockler, J. H. Chang
Referenced in: 1 Publication (2016)
Related Software: Scotty; PROPER; DEseq; DEGseq; SAS; Bioconductor
Main Fields: Biology and other natural sciences (92-XX)

GeneFriends

Software Authors:   van Dam, S.; Craig, T.; de Magalhaes, J. P.
Referenced in: 1 Publication (2020)
Related Software: PLANEX; COXPRESdb; TGCnA; clusterProfiler; GitHub; KEGG; …
Main Fields: Statistics (62-XX)

goseq

Software Authors:   Matthew Young
Referenced in: 1 Publication (2016)
Related Software: sydSeq; GSAASeqSP; gage; ROAST; GSVA; Voom; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

GSAASeqSP

Software Authors:   Xiong , Q. Mukherjee , S. Furey
Referenced in: 1 Publication (2016)
Related Software: sydSeq; goseq; gage; ROAST; GSVA; Voom; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

GSNAP

Software Authors:   Thomas D. Wu, Jens Reeder, Michael Lawrence, Gabe Becker, Matthew J. Brauer
Referenced in: 1 Publication (2016)
Related Software: Galaxy; ROAST; featureCounts; Rsubread; recount; PROPER; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

GUESSmyLT

Software Authors:   Erik Berner Wik; Hampus Olin; Caitlin Vigetun Haughey; Lisa Klasson; Jacques Dainat
Referenced in: 0 Publications
Related Software: BUSCO; TRINITY; Bowtie 2; RSeQC; Python
Main Fields:

HmmSeq

Software Authors:   Cui, Shiqi; Guha, Subharup; Ferreira, Marco A.R.; Tegge, Allison N.
Referenced in: 1 Publication (2015)
Related Software: DAVID; BaySeq; CNAmet; tmvtnorm; edgeR; Bioconductor; …
Main Fields: Statistics (62-XX)

HMMSplicer

Software Authors:   Dimon, M.T.; Sorber, K.; DeRisi, J.L.
Referenced in: 1 Publication (2012)
Related Software: ARACHNE; SpliceTrap; DWE; CLIPZ; mirTools; miRExpress; …
Main Fields: General and overarching topics; collections (00-XX); Biology and other natural sciences (92-XX)

intePareto

Software Authors:   Yingying Cao
Referenced in: 1 Publication (2021)
Related Software: STAR; iClusterPlus; BiSeq; MethylSeekR; rGREAT; rGADEM; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

IUTA

Software Authors:   Niu, L., Huang, W., Umbach, D. M., Li, L.
Referenced in: 1 Publication (2018)
Related Software: DESeq2; rSeqDiff; EBSeq; TopHat; ShrinkBayes; BaySeq; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

LSC

Software Authors:   Au, K.F., Underwood, J.G., Lee, L., Wong, W.H.
Referenced in: 1 Publication (2019)
Related Software: d2_cluster; Rainbow; SlideSort; Mash; Corset; Grouper; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

MAP-RSeq

Software Authors:   Kalari KR, Nair AA, Bhavsar JD, O’Brien DR, Davila JI, Bockol MA, Nie J, Tang X, Baheti S, Doughty JB, Middha S, Sicotte H, Thompson AE, Asmann YW, Kocher JP
Referenced in: 1 Publication (2017)
Related Software: BWA; BatMeth; PSAR-Align; CAP-miRSeq; Pash; Socrates; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

MATHT

Software Authors:   Song, Wei; Liu, Huaping; Wang, Jiajia; Kong, Yan; Yin, Xia; Zang, Weidong
Referenced in: 1 Publication (2018)
Related Software: SolexaQA; miRecords; DNMAD; FunCoup; miTarget; TopHat-Fusion; …
Main Fields: Computer science (68-XX); Biology and other natural sciences (92-XX)

MITIE

Software Authors:   Jonas Behr; André Kahles; Yi Zhong; Vipin T. Sreedharan; Philipp Drewe; Gunnar Rätsch
Referenced in: 1 Publication (2018)
Related Software: CLIIQ; WemIQ; GENCODE; RSEM; TopHat; casper
Main Fields: Statistics (62-XX)

MultiTrans

Software Authors:   Jin Zhao, Haodi Feng, Daming Zhu, Yu Lin
Referenced in: 1 Publication (2022)
Related Software: Gurobi; Scallop2; ShoRAH; SSP; StringTie; RefShannon; …
Main Fields: Operations research, mathematical programming (90-XX); Biology and other natural sciences (92-XX)

NGS-QC

Software Authors:   –
Referenced in: 1 Publication (2016)
Related Software: Galaxy; ROAST; featureCounts; Rsubread; recount; PROPER; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

NGS-Trex

Software Authors:   Ilenia Boria, Lara Boatti, Igor Saggese, Flavio Mignone
Referenced in: 1 Publication (2015)
Related Software: EMIRGE; ViennaRNA; TagCleaner; OligoWalk; OptiRNAi; ASTALAVISTA; …
Main Fields: General and overarching topics; collections (00-XX); Biology and other natural sciences (92-XX)

Omics Pipe

Software Authors:   Fisch KM, Meissner T, Gioia L, Ducom JC, Carland TM, Loguercio S, et al.
Referenced in: 0 Publications
Related Software: Anaconda; IPython; PyPI; BioRuby; BioSQL; BioJava; …
Main Fields:

Orione

Software Authors:   Gianmauro Cuccuru, Massimiliano Orsini, Andrea Pinna, Andrea Sbardellati, Nicola Soranzo, Antonella Travaglione, Paolo Uva, Gianluigi Zanetti, Giorgio Fotia
Referenced in: 1 Publication (2016)
Related Software: PlantTFDB; eggNOG; ELM; dbCAN; antiSMASH; dissectHMMER; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

PALMapper

Software Authors:   Andre Kahles; Gunnar Rätsch
Referenced in: 1 Publication (2018)
Related Software: HaploReg; MapSplice; eSNV-detect; Strelka; Salmon; ZOOM; …
Main Fields: Biology and other natural sciences (92-XX)

pasilla

Software Authors:   Huber, W.; A. Reyes
Referenced in: 1 Publication (2018)
Related Software: adaptMT; AdaPT; Genefilter; GEOquery
Main Fields: Statistics (62-XX)

Pathomic Fusion

Software Authors:   Richard J. Chen, Ming Y. Lu, Jingwen Wang, Drew F. K. Williamson, Scott J. Rodig, Neal I. Lindeman, Faisal Mahmood
Referenced in: 1 Publication (2021)
Related Software: Grad-CAM; Microscope; pyjive; GitHub; ImageNet; PyTorch; …
Main Fields: Statistics (62-XX)

PGTools

Software Authors:   Nagaraj, S. H.; Waddell, N.; Madugundu, A. K.; Wood, S.; Jones, A.; Mandyam, R. A.; Nones, K.; Pearson, J. V.; Grimmond, S. M.
Referenced in: 0 Publications
Related Software: GeneScout; iPiG; KNIME; MyriMatch; Peppy; PGx; …
Main Fields:

PINCAGE

Software Authors:   Świtnicki, M. P., M. Juul, T. Madsen, K. D. Sørensen, J. S. Pedersen
Referenced in: 1 Publication (2019)
Related Software: DESeq2; FastDMA; ChAMP; arm; Minfi; ASCL; …
Main Fields: Statistics (62-XX); Biology and other natural sciences (92-XX)

polyester

Software Authors:   Alyssa C. Frazee, Andrew E. Jaffe, Rory Kirchner, Jeffrey T. Leek
Referenced in: 0 Publications
Related Software: VCNet; edgeR; ARACNE; DEseq; JDINAC; DINGO; …
Main Fields:

powsimR

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

PUseqClust

Software Authors:   Shi, Xianfeng; Liu, Xuejun; Zhang, Li
Referenced in: 1 Publication (2019)
Related Software: mclust
Main Fields: Statistics (62-XX); Computer science (68-XX); Biology and other natural sciences (92-XX)