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 tTt and qTfy enable single- cell tracking and quantification of cellular and molecular properties in time-lapse imaging data. Reference: Hilsenbeck et al, Nat. Biotechnol. 34, 703-706 (2016), DOI: 10.1038/nbt.362 

destiny: An R library for diffusion maps
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MCA: A visualization method for correlated subpopulations
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MONA: A new method for investigating biological functions across multiple "omics" levels via integrated GO enrichment
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GPLVM for time-structured gene-expression data
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D2D Software: A collection of numerical methods for quantitative dynamic modeling of biochemical processes, which provides reliable and efficient model calibration methods
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stochprofML: Parameterize cell-to-cell regulatory heterogeneities using stochastic profiling and maximum likelihood estimation
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Odefy: From discrete to continuous models
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PhenomiR: A knowledgebase for microRNA expression in diseases and biological processes
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simbTUM: Simulation of stochastic processes and ODE models in biology
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bioSDP: A Matlab Toolbox for the analysis of uncertain biochemical networks via semidefinite programming
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zfishDB uses links between orthologous genes to retrieve hypothetical interactions between zebrafish genes
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Gepard: A very fast dotplotting tool for the comparisons of two genome sequences
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GraDe: Knowledge-based matrix factorization
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CSA: colored subspace analysis
Vertex Centralities in Input-Output Networks
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miRco: miRco predicts cooperatively targeted mRNAs based on binding site distances
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