Tools   Select Another Resource Report Type

http://biolemmatizer.sourceforge.net/

A domain-specific lemmatization software tool for the morphological analysis of biomedical literature.

Proper citation: BioLemmatizer (RRID:SCR_000117) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/exomesuite/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software application designed to analyze variant call files from next generation sequencing data to identify variants causing disease.

Proper citation: exomeSuite (RRID:SCR_000129) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/kanalyze/

A Java toolkit designed to convert DNA and RNA sequences into k-mers.

Proper citation: KAnalyze (RRID:SCR_001323) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/glprobs/

Software implementing a simple and effective approach to improve the accuracy of multiple sequence alignment.

Proper citation: GLProbs (RRID:SCR_002739) Copy   

•   Source: SciCrunch Registry

http://rdock.sourceforge.net/

A fast and versatile Open Source docking software program that can be used to dock small molecules against proteins and nucleic acids.

Proper citation: rDock (RRID:SCR_002838) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ms-spectre/

Software that provides (Quantitiave) analysis of multiple ls-ms(ms) runs, using mzXML import of raw data coming from spectrometers.

Proper citation: MS-Spectre (RRID:SCR_000266) Copy   

•   Source: SciCrunch Registry

http://ribopicker.sourceforge.net/

Software to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets.

Proper citation: riboPicker (RRID:SCR_000360) Copy   

•   Source: SciCrunch Registry

http://parsecnv.sourceforge.net/

Software that takes CNV calls as input and creates SNP based statistics for CNV occurrence in cases and controls then calls CNVRs based on neighboring SNPs of similar significance.

Proper citation: ParseCNV (RRID:SCR_000355) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/kinannote/

Software that identifies and classifies protein kinases in a user-provided fasta file using an HMM derived from serine / threonine protein kinases, a position specific scoring matrix derived from the HMM, and comparison with a local version of the curated kinase database from kinase.com.

Proper citation: Kinannote (RRID:SCR_000352) Copy   

•   Source: SciCrunch Registry

http://proteinprophet.sourceforge.net/

Software that automatically validates protein identifications made on the basis of peptides assigned to MS/MS spectra by database search programs such as SEQUEST.

Proper citation: ProteinProphet (RRID:SCR_000286) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/fingerid/

A metabolite identification software using tandem mass spectrometry and kernel methods.

Proper citation: FingerID (RRID:SCR_012077) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/netmode/

Fast motif detection algorithm for subgraph size no more than 6.

Proper citation: NetMODE (RRID:SCR_012085) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/hopemap/

A connected-components based fast algorithm for network alignment.

Proper citation: HopeMap (RRID:SCR_012081) Copy   

•   Source: SciCrunch Registry

http://glare.sourceforge.net/

A software that facilitates and improves the design of chemical combinatorial libraries.

Proper citation: GLARE (RRID:SCR_012083) Copy   

•   Source: SciCrunch Registry

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