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http://sourceforge.net/projects/hopemap/
A connected-components based fast algorithm for network alignment.
Proper citation: HopeMap (RRID:SCR_012081) Copy
http://sourceforge.net/projects/mcdl/
A small Java molecular viewer/editor for chemical structures, stored in Modular Chemical Descriptor Language linear notation.
Proper citation: MCDL (RRID:SCR_012084) Copy
A software that facilitates and improves the design of chemical combinatorial libraries.
Proper citation: GLARE (RRID:SCR_012083) Copy
Software that allows fast and user-friendly verification of Mascot result files, as well as data quantification using isotopic labeling methods (SILAC/ICAT) or label free approaches (spectral counting, MS signal comparison).
Proper citation: MFPaQ (RRID:SCR_012049) Copy
http://proteowizard.sourceforge.net/
Software that enables rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard proteomics and LCMS dataset computations.
Proper citation: ProteoWizard (RRID:SCR_012056) Copy
http://sourceforge.net/projects/adtex/
A software tool for copy number variation (CNV) detection for whole-exome data from paired tumour/matched normal samples.
Proper citation: ADTEx (RRID:SCR_012059) Copy
http://sourceforge.net/projects/multiplierz/
An open-source Python-based environment that provides a scriptable framework for efficient access to manufacturers'' proprietary data files via mzAPI.
Proper citation: multiplierz (RRID:SCR_012058) Copy
http://sourceforge.net/projects/te-locate/
A software tool to locate all copies of sequences in a reference sequence using read-pairs.
Proper citation: TE-locate (RRID:SCR_012063) Copy
http://sourceforge.net/projects/laitor/
A text mining software developed to find co-occurrence of biological entities (gene/protein terms) together with biointeractions and concepts term from customized dictionaries.
Proper citation: LAITOR (RRID:SCR_012101) Copy
http://matnmr.sourceforge.net/
A highly flexible software toolbox for processing 1D and 2D NMR and EPR spectra under MATLAB, creating high-quality 1D, 2D or 3D plots from the spectra and printing them in every type of format that is supported by MATLAB.
Proper citation: MatNMR (RRID:SCR_012060) Copy
http://mzmine.sourceforge.net/
Software for mass-spectrometry data processing, with the main focus on LC-MS data.
Proper citation: MZmine (RRID:SCR_012040) Copy
http://sourceforge.net/projects/exorca/
A Matlab package extending the scope of established COBRA metabolic modelling.
Proper citation: ORCA (RRID:SCR_012097) Copy
http://opencobra.sourceforge.net/openCOBRA/Welcome.html
Software Python package that provides support for basic COnstraint-Based Reconstruction and Analysis (COBRA) methods.
Proper citation: COBRApy (RRID:SCR_012096) Copy
http://knowtator.sourceforge.net/
A general-purpose text annotation tool that is integrated with the Prot����g���� knowledge representation system.
Proper citation: Knowtator (RRID:SCR_012099) Copy
http://sourceforge.net/projects/pb-jelly/
Software that automates the finishing process using long sequence reads in a reference-guided assembly process.
Proper citation: PBJelly (RRID:SCR_012091) Copy
http://contra-cnv.sourceforge.net/
A tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data.
Proper citation: CONTRA (RRID:SCR_010814) Copy
http://svdetect.sourceforge.net/Site/Home.html
Software 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. This tool aims to identify structural variations with both clustering and sliding-window strategies, and helping in their visualization at the genome scale. It is compatible with SOLiD and Illumina (>=1.3) reads.
Proper citation: SVDetect (RRID:SCR_010812) Copy
http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=Main_Page
A de novo whole-genome shotgun (WGS) DNA sequence assembler.
Proper citation: Celera assembler (RRID:SCR_010750) Copy
http://sourceforge.net/apps/mediawiki/vancouvershortr/index.php?title=FindPeaks
Software application that can be used for converting Eland, Maq (.map), BED or other files into WIG files and identifying areas of enrichment (ChIP-Seq analysis).
Proper citation: FindPeaks (RRID:SCR_010857) Copy
http://genovar.sourceforge.net/
A Detection and Visualization software tool for Genomic Variants.
Proper citation: Genovar (RRID:SCR_010930) Copy
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