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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/dynamicprog/
A model-based statistical methods for base calling in Illumina''s next-generation sequencing platforms.
Proper citation: DynamicProg (RRID:SCR_013217) Copy
Software for a normalization scheme that corrects nucleotide composition bias, mappability variations and differential local DNA structural effects in deep sequencing data.
Proper citation: BEADS (RRID:SCR_013229) Copy
http://sourceforge.net/projects/congrpe/
A de novo assembly algorithm for Next-Generation Sequencing technology.
Proper citation: CongrPE (RRID:SCR_013190) Copy
http://sourceforge.net/projects/callsim/
A software application that provides evidence for the validity of base calls believed to be sequencing errors and it is applicable to Ion Torrent and 454 data.
Proper citation: CallSim (RRID:SCR_013192) Copy
http://sourceforge.net/projects/sapas/
A RNA-seq method for polyA research.
Proper citation: SAPAS (RRID:SCR_013195) Copy
http://arrayoligosel.sourceforge.net/
Software program to systematically design gene specific long oligonucleotide probes for entire genomes, for the purpose of developing whole genome microarrays. For each open reading frame, the program optimizes the oligo selection based upon several parameters, including uniqueness in the genome, sequence complexity, lack of self-binding, GC content and proximity to the 3''end of the gene.
Proper citation: ArrayOligoSelector (RRID:SCR_013494) Copy
http://denovoassembler.sourceforge.net/
Software for a massively distributed metagenome assembler that is coupled with Ray Communities, which profiles microbiomes based on uniquely-colored k-mers.
Proper citation: Ray Meta (RRID:SCR_011918) Copy
http://uc-echo.sourceforge.net/
Error correction algorithm designed for short-reads from next-generation sequencing platforms such as Illumina''s Genome Analyzer II.
Proper citation: ECHO (RRID:SCR_011851) Copy
http://tagcleaner.sourceforge.net/
A software tool which can automatically detect and efficiently remove tag sequences from genomic and metagenomic datasets.
Proper citation: TagCleaner (RRID:SCR_011846) 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
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