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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://sourceforge.net/projects/mmax2/
A GUI-based text annotation tool for creating and visualizing annotations.
Proper citation: MMAX2 (RRID:SCR_012100) Copy
http://ipapers.sourceforge.net/iPapers.html
Software application that manages many PDF files of articles, whose information can be obtained by PubMed.
Proper citation: iPapers (RRID:SCR_012103) Copy
http://sourceforge.net/projects/phylotreepruner/
A utility that uses a phylogenetic approach to refine orthology inferences made by graph-based (or other) methods.
Proper citation: PhyloTreePruner (RRID:SCR_012069) Copy
http://sourceforge.net/projects/coperead/
An efficient software tool to connect overlapping pair-end reads using k-mer frequencies.
Proper citation: Connecting Overlapped Pair-End reads (RRID:SCR_012102) Copy
http://sourceforge.net/projects/raspnmr/
Software that uses structure-based chemical shift predictions to solve the backbone resonance assignment problem in protein NMR spectroscopy.
Proper citation: RASP (RRID:SCR_012062) Copy
http://sourceforge.net/projects/gsim/
Free software tool for visualisation and processing of experimental and simulated nuclear magnetic resonance (NMR) spectra.
Proper citation: GSim (RRID:SCR_012061) Copy
http://sourceforge.net/projects/staden/
A C software implementation of SAM, BAM and CRAM file I/O.
Proper citation: Scramble (RRID:SCR_012036) Copy
http://mzmatch.sourceforge.net/mzmatch.R/mzmatch.ipeak.align.CowCoda.html
Software that performs retention time alignment on the given set of peaks.
Proper citation: CowCoDA (RRID:SCR_012039) Copy
http://sourceforge.net/projects/open-ms/
An algorithm to align LC-MS samples and to match corresponding ion species across samples.
Proper citation: OpenMS (RRID:SCR_012042) Copy
http://obi-warp.sourceforge.net/
Software that aligns matrices along a single axis using Dynamic Time Warping (DTW) and a one-to-one (bijective) interpolated warp function.
Proper citation: OBI-Warp (RRID:SCR_012041) Copy
http://open-ms.sourceforge.net/
THIS RESOURCE IS NO LONGER IN SERVICE.Documented on May 23rd,2023. Software that provides a set of computational tools which can be easily combined into analysis pipelines even by non-experts and can be used in proteomics workflows.
Proper citation: TOPP (RRID:SCR_012044) Copy
http://open-ms.sourceforge.net/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23rd,2023. Software that combines Lagrangian relaxation for solving an integer linear programming formulation with an adaptation of Yen''s k shortest paths algorithm.
Proper citation: Antilope (RRID:SCR_012046) Copy
http://sourceforge.net/projects/swisspit/
Software for pipelined analysis of mass spectrometry data.
Proper citation: swissPIT (RRID:SCR_012045) Copy
http://sourceforge.net/projects/icplquant/
A proteomics software tool for quantitatively analyzing large mass spectrometric datasets acquired from ICPL based proteomics experiments.
Proper citation: ICPL ESIQuant (RRID:SCR_012047) Copy
http://sourceforge.net/projects/mtoolbox/
Software for a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data.
Proper citation: MToolBox (RRID:SCR_012112) Copy
http://revister.sourceforge.net/
Software for an automated pipeline using a ''local mapping reference reconstruction method'' to revise mismapped or partially misaligned reads at simple tandem repeat loci.
Proper citation: ReviSTER (RRID:SCR_012113) Copy
http://sourceforge.net/projects/virtools/
Software for a low frequency Virus Variant detection pipeline for Illumina data.
Proper citation: VirVarSeq (RRID:SCR_012116) Copy
http://sourceforge.net/projects/pegasus-fus/
Software that annotates biologically functional gene fusion candidates.
Proper citation: Pegasus-fus (RRID:SCR_012118) Copy
http://sourceforge.net/projects/nailsystemsbiology/
A set of software tools to simplify the range of computational activities involved in regulatory network inference. It is technology-independent and includes an interface layer to allow easy integration of components into other applications. It is implemented in MATLAB and is available for all researchers to use.
Proper citation: NAIL (RRID:SCR_012134) Copy
http://sourceforge.net/projects/imsat/
A python program that uses the polymorphism data obtained from mapping individual Illumina sequence reads onto a reference genome to identify polymorphic STRs.
Proper citation: iMSAT (RRID:SCR_012135) Copy
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