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http://mfpaq.sourceforge.net/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/exorca/

A Matlab package extending the scope of established COBRA metabolic modelling.

Proper citation: ORCA (RRID:SCR_012097) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://seqpig.sourceforge.net/

A software library for Apache Pig for the distributed analysis of large sequencing datasets on Hadoop clusters.

Proper citation: SeqPig (RRID:SCR_008548) Copy   

•   Source: SciCrunch Registry

http://geckoe.sourceforge.net/

A complete, high-capacity centralized gene expression analysis system, developed in response to the needs of a distributed user community.

Proper citation: Gecko (RRID:SCR_009001) Copy   

•   Source: SciCrunch Registry

http://scalce.sourceforge.net/Home

A FASTQ compression tool that uses locally consistent parsing to obtain better compression rate.

Proper citation: SCALCE (RRID:SCR_009658) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/apps/mediawiki/cdao/

A formalization of concepts and relations relevant to evolutionary comparative analysis, such as phylogenetic trees, OTUs (operational taxonomic units) and compared characters (including molecular characters as well as other types). CDAO is being developed by scientists in biology, evolution, and computer science

Proper citation: Comparative Data Analysis Ontology (RRID:SCR_010297) Copy   

•   Source: SciCrunch Registry

http://genotan.sourceforge.net/

A free software tool to identify length variation of microsatellites from short sequence reads.

Proper citation: GenoTan (RRID:SCR_007935) Copy   

•   Source: SciCrunch Registry

http://brig.sourceforge.net/

A cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data.

Proper citation: BRIG (RRID:SCR_007802) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bamstats/

A GUI desktop tool for calculating and displaying metrics to assess the success of Next Generation Sequencing mapping tools. BAMstats is written in Java and based around the Picard API.

Proper citation: BAMStats (RRID:SCR_006973) Copy   

•   Source: SciCrunch Registry

http://seqbarracuda.sourceforge.net/

A sequence mapping software that utilizes the massive parallelism of graphics processing units to accelerate the inexact alignment of short sequence reads to a particular location on a reference genome. It can align a paired-end library containing 14 million pairs of 76bp reads to the Human genome in about 27 minutes (from fastq files to SAM alignment) using a ��380 NVIDIA Geforce GTX 680*. The alignment throughput can be boosted further by using multiple GPUs (up to 8) at the same time. Being based on BWA (http://bio-bwa.sf.net) from the Sanger Institute, BarraCUDA delivers a high level of alignment fidelity and is comparable to other mainstream alignment programs. It can perform gapped alignment with gap extensions, in order to minimise the number of false variant calls in re-sequencing studies.

Proper citation: BarraCUDA (RRID:SCR_006881) Copy   

•   Source: SciCrunch Registry