Tools for network structure analysis, browsing and simulations:

ACSN: Atlas of Cancer Signaling Network

ACSN is a pathway database and a web-based environment that contains a collection of interconnected cancer-related signalling network maps and allows omics data visualization and analysis.

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NaviCell: browsing large networks using Google Maps

A web tool and a web service for exploring large maps of molecular interactions and visualizing data on top of them.

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BiNoM: Biological Network Manager

BiNoM is a Cytoscape plugin, developed to facilitate the manipulation of biological networks represented in standard systems biology formats (SBML, SBGN, BioPAX) and to carry out studies on the network structure. BiNoM provides the user with a complete interface for the analysis of biological networks in Cytoscape environment.

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MaBoSS: Boolean netwok model simulator

MaBoSS is a C++ software for simulating continuous/discrete time Markov processes, applied on a Boolean network.

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DeDaL: data-driven network layouts

DeDaL is a Cytoscape 3.0 app which uses several algorithms of dimention reduction to produce data-driven network layouts based on multidimensional data (typicaly gene expression)..

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NETI: network reverse engineering

Generalized approach for the reconstruction of regulatory networks from time-series data. This approach uses elements of control theory and the space-state formalism to approximate interactions between two observable nodes (e.g. measured genes).

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OCSANA: computing optimal minimal cut sets for complex and large networks

OCSANA (Optimal Combinations of Interventions from Network Analysis) is a new software designed to identify and prioritize optimal and minimal, combinations of interventions to disrupt the paths between source nodes and target nodes.

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Tools for omics data analysis:

ROMA: Calculation of gene set activities from omics data

ROMA is a software package written in Java for the quantification and representation of biological module activity using gene expression or other omics data.

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NaviCom: bridge betweem cBioPortal and ACSN databases

A web-based application for generating interactive network based molecular portraits using high-throughput datasets, using NaviCell

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ACSNmineR: Gene Enrichment Analysis from ACSN Maps

Computing and represent gene set enrichment or depletion from user data based on the molecular interaction maps from the Atlas of Cancer Signalling Network (ACSN) or maps imported by a user.

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ViDaExpert: 3D interface for data visualization

ViDaExpert is a user-friendly tool for nonlinear visualization and analysis of multidimensional vectorial data. It implements standard methods such as PCA, but also non-linear versions of principal manifolds. ViDaExpert is equipped with convinient 3D user interface.

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ElMap: non-linear principal manifolds

elmap - is a tool for fast construction of non-linear principal manifolds of various topologies in multidimensional data space, for a discrete set of weightened points.

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Tools for NGS data analysis:

Control-FREEC: copy number and genotype caller

Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data.

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MICSA: Motif Identification for ChIP-Seq Analysis

MICSA is package for the identification of transcription factor binding sites in ChIP-Seq data

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Nebula: Galaxy pipeline for ChiP-Seq Analysis

A web service provided by Institut Curie and powered by Galaxy which allows users (Bioinformaticians as far as Biologists) to analyze their ChIP-seq data.

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SV-Bay: structural variant detection in cancer genomes

Structural variant detection in cancer genomes using a Bayesian approach with correction for GC-content and read mappability.

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RNFTools: NGS read mapper evaluator

RNFTools simplifies evaluation of read mappers and debugging of tools for NGS data analysis...

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SVDetect: genomic structural variations detector

SVDetect is an application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies

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