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  • ZINBWaVE: Zero-Inflated Negative Binomial based Wanted Variation Extraction
  • HiC-Pro : An optimized and flexible pipeline for Hi-C processing
  • [PASTIS]: Poisson-based Algorithm for STable Inference of DNA Structure
  • [FlipFlop]: Fast Lasso-based Isoform Prediction as a Flow Problem
  • [TIGRESS]: Trustful inference of gene regulation using stability selection
  • [ProDiGe]: Prioritization of disease genes
  • [GFLseg]: Group fused lasso for signal segmentation
  • [ClusterPath]: Clustering using convex fusion penalties
  • [FREEC]: Control-FREE Copy number caller from deep-sequencing data
  • [GraphM]: Graph matching package
  • [PARIS]: Pocket Alignment in Relation to Identification of Substrates
  • [SIRENE]: Supervised Inference of REgulatory NEtwork
  • [KISS]: MHC-I epitope prediction
  • [GAkernel]: Global alignment kernel for time series comparison
  • [DSIR]: design of siRNA
  • [ChemCpp]: a C++ toolbox for chemoinformatics integrating the computation of kernels functions between chemical compounds
  • [SLP-Local]: prediction of protein subcellular localization from their amino-acid sequence with support vector machines
  • [NGrid]: open source grid computing framework