Softwares

ZINB-WaVe - Zero-inflated negative binomial model for RNA-seq data

ZINB-WaVe is an R package for dimension reduction and factor analysis on single-cell RNA-seq data.

PASTIS - Poisson-based Algorithm for STable Inference of DNA Structure

PASTIS is not a drink. It is a free Python implementation of methods to infer the 3D structure of a genome from Hi-C data.

FlipFlop - Fast Lasso-based Isoform Prediction as a Flow Problem

FlipFlop is a fast method for de novo transcript discovery and abundance estimation from RNA-Seq data.

TIGRESS - Trustful Inference of Gene REgulation using Stability Selection

TIGRESS is a free MATLAB implementation of a method to infer regulatory networks from gene expression data.

ProDiGe - Prioritization of disease genes

ProDiGe is a free MATLAB implementation of an algorithm for gene prioritization or gene ranking

GFLseg - Group fused lasso for signal segmentation

GFLseg is a MATLAB implementation of the group fused Lasso method to detect multiple change-points in a multidimensional signal.

ClusterPath - Clustering using convex fusion penalties

This is an R/C++ implementation of a clustering method that can be thought of as a convex relaxation of K-means (implementation by Toby Hocking)

FREEC - Control-FREE Copy number caller

FREEC is a tool for control-free copy number alteration (gains and losses) detection from deep-sequencing data, using normalization on GC-content.

GraphM - Graph Matching package

GraphM is a tool for approximate solving of large scale graph matching problems. The idea is to collect together different graph matching methods which have been proposed in the last ten years, and to organize them in a simple, easily extendible software package. (implementation by Mikhail Zaslavskiy)

PARIS - Pocket Alignment in Relation to Identification of Substrates

PARIS implements a new protein binding pocket similarity measure based on comparison of 3D atom clouds, for the purpose of ligand prediction.

SIRENE - Supervised Inference of REgulatory NEtwork

A MATLAB implementation of SIRENE that allows you in reconstruct missing regulations in a regulatory network given expression data.

KISS - MHC-I epitope prediction

KISS (Kernel-based Inter-allele peptide binding prediction SyStem) is a server that predicts epitopes of MHC-I molecules for a variety of different alleles. It is based on a multitask support vector machine. (implementation by Laurent Jacob)

GAkernel - Global alignment kernel

This is C/MATLAB implementation of the global alignment kernel between time series (similar but better than dynamic time warping), written by Marco Cuturi.

DSIR - Design of siRNA

DSIR (Design of siRNA) helps you design your siRNA by predicting their efficacy. It is based on a sparse linear model based on sequence features.

ChemCPP - Kernels for small molecules

ChemCpp is a C++ toolbox for chemoinformatics focusing on the computation of kernel functions between chemical compounds.

SLP-local - Protein subcellular localization prediction

SLP-local is a server for the prediction of protein subcellular localization from their amino-acid sequence with support vector machines

LAKernel - Local alignment kernels

The local alignment kernel is a similarity score between biological sequences. Combined with support vector machines it leads to very good performance for remote homology detection, and might be useful for other applications as well. This C code should allow you to compute the local alignment kernel between protein sequences encoded in FASTA file. Reference
[1] J.-P. Vert, H. Saigo, T. Akutsu, Local alignment kernels for biological sequences, in Kernel Methods in Computational Biology, B. Schölkopf, K. Tsuda and J.-P. Vert (Eds.), MIT Press, p.131-154, 2004.[pdf]
[2] H. Saigo, J.-P. Vert, T. Akutsu and N. Ueda, Protein homology detection using string alignment kernels, Bioinformatics, vol.20, p.1682-1689, 2004.
Vert Jean-Philippe
Last modified: Fri Mar 14 09:28:38 CET 2008