Showing 13 open source projects for "data base chess"

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  • 1
    Quadric

    Quadric

    Application for simple base-2 binary to base-4 DNA-code conversion

    Quadric is an opensource file converter created by the Jomcraft Network development team. In it's core functionality this small utility can transform base-2 binary files into base-4 DNA-coded human-legible ASCII-files.
    Downloads: 0 This Week
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  • 2

    RNAfdl

    RNA force directed layout

    RNAfdl is a highly flexible tool for drawing RNA secondary structures. Secondary structures can be visualized as classical secondary structure plot, circle plot, linear plot or mountain plot. RNAfdl allows manual editing and several drawing styles, as well as a fully automated conjugate gradients minimization approach to draw more complex structures without user interaction. In addition, RNAfdl allows you to incorporate non-canonical base pairs into drawings.
    Downloads: 1 This Week
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  • 3
    ViralFusionSeq [VFS]

    ViralFusionSeq [VFS]

    Accurately discover viral integration events and fusion transcripts

    VFS was fullly tested under Ubuntu/Debian system. ** Announcement 1**: VFS is superior to Virus-Clip. https://sourceforge.net/projects/viralfusionseq/files/VFS.vs.Virus-Clip.pdf/download As of 2016, VFS is the only viral integration tool available at NIH HPC system. https://hpc.nih.gov/apps/ViralFusionSeq/ ViralFusionSeq (VFS) is a versatile high-throughput sequencing (HTS) tool for discovering viral integration events and reconstruct fusion transcripts at single-base...
    Downloads: 2 This Week
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  • 4

    iCAS - An Illumina Clone Assembly System

    An Illumina clone assembly system using SOAPdenovo and ABySS

    Clone-by-clone sequencing, as a means of achieving high quality assemblies for large and complex genomes, continues to be of great relevance in the era of high throughput sequencing. However, assemblies obtained using current whole genome assemblers are often fragmented and sometimes have issues of genome completeness owing to different data characteristics introduced by multiplexed sequencing. With iCAS the data filtering process is based on a novel kmer frequency algorithm, resulting in near perfect pre-assembly reads. Contigs are generated using different assembly algorithms and then merged together to achieve longer continuity. Re-aligning all the reads back to the draft contigs and recalibrating each sequence base achieves a final consensus. ...
    Downloads: 0 This Week
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  • 5
    VarScan

    VarScan

    Variant detection in next-generation sequencing data

    Variant detection in massively parallel sequencing. For one sample, calls SNPs, indels, and consensus genotypes. For tumor-normal pairs, further classifies each variant as Germline, Somatic, or LOH, and also detects somatic copy number changes. THE LATEST VERSION IS AVAILABLE ON GITHUB
    Downloads: 86 This Week
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  • 6
    A base for programs. Includes algorythms for Q-learning and SOM's etc. too. Examples: Hamron: Simulates evolution, uses the 2D-renderer. DriveUnit: created for school, for a robotic arm, uses the 3D-renderer. Hlearn: http://www.sagenb.org/home/pub/8
    Downloads: 0 This Week
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  • 7

    rnasimulase

    Simulation of allele-specific RNA-seq data

    Simulation of allele-specific RNA-seq data
    Downloads: 0 This Week
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  • 8

    ViNSS View

    Vienna Notation Secondary Structure Viewer

    ViNSS View is a highly flexible tool for drawing RNA secondary structures. Secondary structures can be visualized as classical secondary structure plot, circle plot, linear plot or mountain plot. ViNSS View allows manual editing and several drawing styles, as well as a fully automated conjugate gradients minimization approach to draw more complex structures without user interaction. In addition, ViNSS View allows you to incorporate non-canonical base pairs into your drawing.
    Downloads: 0 This Week
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  • 9
    CallSim

    CallSim

    low-volume read processing base corrector

    CallSim is 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. CallSim provides a final classification or rescue of a base/indel in reads, where putative variants have been identified via typical SNP/indel workflows. plots rendered by: JFreeChart library http://sourceforge.net/projects/jfreechart/
    Downloads: 0 This Week
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  • 10

    HPCall

    Improved base-calling for homopolymer-sensitive next-gen data.

    The current software contains the implementation for the 454 pyrosequencing platform.
    Downloads: 0 This Week
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  • 11
    The BioArray Software Environment (BASE) v1.2 is a comprehensive free web-based database solution for the massive amounts of data generated by microarray analysis. PrognoChip-BASE extends BASE v1.2.16, providing more functionalities.
    Downloads: 0 This Week
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  • 12
    Thea, Tools for High-throughput Experiment Analysis, is an integrated information processing system dedicated to the annotation of data issued from classification systems with biological information coming from a knowledge base.
    Downloads: 1 This Week
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  • 13
    BASE is a database server to manage (locally) the massive amounts of data generated by microarray analysis. It handles biomaterials, raw data and images, and provides integrated and plug-in-able normalization, data viewing and analysis tools.
    Downloads: 0 This Week
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