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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
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
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
http://sourceforge.net/projects/mirplant/
A user-friendly plant miRNA prediction tool.
Proper citation: miRPlant (RRID:SCR_012105) Copy
http://pypedal.sourceforge.net/
A pedigree analysis software package that provides tools for error checking, mathematical analysis, report generation, pedigree simulation, and data visualization.
Proper citation: PyPedal (RRID:SCR_012104) Copy
http://sourceforge.net/projects/simulatepcr/
Software that can be run from the command line for high throughput applications which can calculate all products from large lists of primers and probes compared to a large sequence database such as nt.
Proper citation: Simulate PCR (RRID:SCR_012106) Copy
http://sourceforge.net/projects/sat-assembler/
A targeted gene assembly software program which aims to recover gene families of particular interest to biologists.
Proper citation: SAT-Assembler (RRID:SCR_012108) Copy
http://sourceforge.net/projects/fingerid/
A metabolite identification software using tandem mass spectrometry and kernel methods.
Proper citation: FingerID (RRID:SCR_012077) Copy
http://sourceforge.net/projects/protrac/
A software which detects and analyses piRNA clusters based on quantifiable deviations from a hypothetical uniform distribution regarding the decisive piRNA cluster characteristics.
Proper citation: proTRAC (RRID:SCR_012078) Copy
http://sourceforge.net/projects/netmode/
Fast motif detection algorithm for subgraph size no more than 6.
Proper citation: NetMODE (RRID:SCR_012085) Copy
http://sketchel.sourceforge.net/
An interactive chemical molecule sketching tool, and molecular spreadsheet data entry application.
Proper citation: SketchEl (RRID:SCR_012082) Copy
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
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