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Bookchapters

  • ISBRA 2019: Bioinformatics Research and Applications
    Deep Learning and Random Forest-Based Augmentation of sRNA Expression Profiles
    Jelena Fiosina, Maksims Fiosins, Stefan Bonn
    Conference paper, 09 May 2019

Software

SEA ( https://sea.dzne.de ): SEA, the small RNA expression atlas, is a web application that allows querying, visualization, and analysis of small RNA expression information for over 30.000 small RNAs, over 2000 samples, hundreds of diseases, over 7 organisms, and plenty of tissues and cell types. SEA is fully interactive and lightning fast and a perfect showcase for the 'knowledge-bases' we build.

Oasis & Oasis 2 ( https://oasis.dzne.de ): Oasis, the online analysis of small RNAs, is a web application that allows for the detection, differential expression, and classification analysis of small RNAs. It is interactive, fast, and heavily used in the research community.

Memory Epigenome Browser ( https://memory-epigenome-browser.dzne.de ): The memory epigenome browser allows to select, visualize, and download over 200 cell type-specific epigenetic and transcriptomic datasets before and after learning. It is part of our manuscript on the epigenetic basis of learning and memory (Halder et al. Nature Neuroscience 2016).

GRAND: Graphs as nested dictionaries is a framework that allows for fast and memory efficient graph operations and interactive visualization. It is a free python package that can read many standard graph formats and supports many standard graph operations (e.g. search, shortest path).