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  • SCODE: An efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation
    Hirotaka Matsumoto, Hisanori Kiryu, Chikara Furusawa, Minoru S.H. Ko, Shigeru B.H. Ko, Norio Gouda, Tetsutaro Hayash, Itoshi Nikaido
    bioRxiv 088856; doi: https://doi.org/10.1101/088856
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  • HiC-Spector: A matrix library for spectral and reproducibility analysis of Hi-C contact maps
    Koon-Kiu Yan, Galip Guürkan Yardimci, William S. Noble, Mark Gerstein
    bioRxiv 088922; doi: https://doi.org/10.1101/088922
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  • ConfocalGN: a minimalistic confocal image simulator
    Serge Dmitrieff, François Nédélec
    bioRxiv 088906; doi: https://doi.org/10.1101/088906
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  • Isolator: accurate and stable analysis of isoform-level expression in RNA-Seq experiments
    Daniel C. Jones, Kavitha T. Kuppusamy, Nathan J. Palpant, Xinxia Peng, Charles E. Murry, Hannele Ruohola-Baker, Walter L. Ruzzo
    bioRxiv 088765; doi: https://doi.org/10.1101/088765
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  • SWALO: scaffolding with assembly likelihood optimization
    Atif Rahman, Lior Pachter
    bioRxiv 081786; doi: https://doi.org/10.1101/081786
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  • A SIMPLE pipeline for mapping point mutations
    Guy Wachsman, Jennifer L. Modliszewski, Manuel Valdes, Philip N. Benfey
    bioRxiv 088591; doi: https://doi.org/10.1101/088591
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  • Scalable variational inference for super resolution microscopy
    Ruoxi Sun, Evan Archer, Liam Paninski
    bioRxiv 081703; doi: https://doi.org/10.1101/081703
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  • UNCROSS: Filtering of high-frequency cross-talk in 16S amplicon reads
    Robert C. Edgar
    bioRxiv 088666; doi: https://doi.org/10.1101/088666
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  • GLASS: assisted and standardized assessment of gene variations from Sanger sequence trace data
    Karol Pal, Vojtech Bystry, Tomas Reigl, Martin Demko, Adam Krejci, Tasoula Touloumenidou, Evangelia Stalika, Boris Tichy, Paolo Ghia, Kostas Stamatopoulos, Sarka Pospisilova, Jitka Malcikova, Nikos Darzentas, European Research Initiative on CLL (ERIC) – TP53 Network
    bioRxiv 088401; doi: https://doi.org/10.1101/088401
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  • HiC-bench: comprehensive and reproducible Hi-C data analysis designed for parameter exploration and benchmarking
    Charalampos Lazaris, Stephen Kelly, Panagiotis Ntziachristos, Iannis Aifantis, Aristotelis Tsirigos
    bioRxiv 084954; doi: https://doi.org/10.1101/084954
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