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  1. 2761
    “…Currently, libraries in Python, R and Perl are available, whilst such for JavaScript are lacking. …”
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    biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) format
  2. 2762
    “…AVAILABILITY AND IMPLEMENTATION: Pathway Inspector is available at the website http://admiral.fmach.it/PI and has been developed in Python, making use of the Django Web Framework.…”
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    Pathway Inspector: a pathway based web application for RNAseq analysis of model and non-model organisms
  3. 2763
    “…AVAILABILITY AND IMPLEMENTATION: INTEGRATE-Neo is implemented in C ++ and Python. Full source code and installation instructions are freely available from https://github.com/ChrisMaherLab/INTEGRATE-Neo. …”
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    INTEGRATE-neo: a pipeline for personalized gene fusion neoantigen discovery
  4. 2764
    por Gosmann, Jan, Eliasmith, Chris
    Publicado 2017
    “…While this does not beat the specialized OpenCL implementation of Nengo, this optimization is available on any platform that can run Python. In contrast, the OpenCL implementation supports fewer platforms and can be difficult to install.…”
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    Automatic Optimization of the Computation Graph in the Nengo Neural Network Simulator
  5. 2765
    “…Overall, this work provides ClinVar data in a format that is easier to work with and can be directly loaded into a variety of popular analysis tools such as R, python pandas, and SQL databases.…”
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    ClinVar data parsing
  6. 2766
    por Eryilmaz, Kerem, Little, Hannah
    Publicado 2016
    “…Theexperimental interface was built using free, and mostly open- source libraries in Python. We provide our sourcecode for other researchers as open source.…”
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    Using leap motion to investigate the emergence of structure in speech and language
  7. 2767
    “…DA+ consists of distributed services and components written in Python and Java, which communicate via messaging and streaming technologies. …”
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    DA+ data acquisition and analysis software at the Swiss Light Source macromolecular crystallography beamlines
  8. 2768
    “…Here, we present TreeTime, a Python-based framework for phylodynamic analysis using an approximate Maximum Likelihood approach. …”
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    TreeTime: Maximum-likelihood phylodynamic analysis
  9. 2769
    “…AVAILABILITY AND IMPLEMENTATION: The tools are written in Python3 and R under the GPLv3 Licence and can be found at https://github.com/itsmeludo/Phyloligo/. …”
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    PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies
  10. 2770
    “…EMHP provides a data preprocessing platform in a small package that requires minimal python dependencies to function. AVAILABILITY AND IMPLEMENTATION: https://www.bitbucket.org/chazbot/emhp Apache 2.0 License SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.…”
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    EMHP: an accurate automated hole masking algorithm for single-particle cryo-EM image processing
  11. 2771
    “…The chewBBACA software uses Python 3.4 or higher and can run on a laptop or in high performance clusters making it useful for both small laboratories and large reference centers. …”
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    chewBBACA: A complete suite for gene-by-gene schema creation and strain identification
  12. 2772
    “…D-GENIES is an easy-to-install, open-source software package (GPL) developed in Python and JavaScript. The source code is available at https://github.com/genotoul-bioinfo/dgenies and it can be tested at http://dgenies.toulouse.inra.fr/.…”
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    D-GENIES: dot plot large genomes in an interactive, efficient and simple way
  13. 2773
    por Loney, Fred, Wu, Guanming
    Publicado 2018
    “…We describe a use case to demonstrate the use of this API in a Python-based notebook, and believe the new API will provide the community a convenient and powerful tool to perform pathway- and network-based data analysis and visualization using our app in an automatic way.…”
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    Automation of ReactomeFIViz via CyREST API
  14. 2774
    por Savalia, Shalin, Emamian, Vahid
    Publicado 2018
    “…The TensorFlow library that was established by Google for deep learning and machine learning is used in python to acquire the algorithms proposed here. The ECG databases accessible at PhysioBank.com and kaggle.com were used for training, testing, and validation of the MLP and CNN algorithms. …”
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    Cardiac Arrhythmia Classification by Multi-Layer Perceptron and Convolution Neural Networks
  15. 2775
    “…FINDINGS: Clinker is a bioinformatics tool written in Python, R, and Bpipe that leverages the superTranscript method to visualize fusion genes. …”
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    Clinker: visualizing fusion genes detected in RNA-seq data
  16. 2776
    por Huynh, Trung, Xu, Sen
    Publicado 2019
    “…GAEV runs on a Windows or Linux system equipped with Python 3 and provides easy accessibility to users with no prior Unix command line experience.…”
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    Gene Annotation Easy Viewer (GAEV): Integrating KEGG’s Gene Function Annotations and Associated Molecular Pathways
  17. 2777
    “…We present benchmark numerical simulations that has been generated from the HOMsPY (Higher Order Methods in Python) library. These results provide detailed information of the underlying Hamiltonian system. …”
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    Numerical simulations for the Toda lattices Hamiltonian system: Higher order symplectic illustrative perspective
  18. 2778
    “…AVAILABILITY AND IMPLEMENTATION: TEPIC is implemented in C++, R, and Python. It is freely available at https://github.com/SchulzLab/TEPIC and can be used on Linux based systems. …”
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    TEPIC 2—an extended framework for transcription factor binding prediction and integrative epigenomic analysis
  19. 2779
    “…The data also include four attached files: 1) time-normalized pitch contours for all speakers (Appendix A), 2) aggregated data of duration, mean intensity, and maximum pitch for on-focus effects (Appendix B), 3) a Python script automatically generating target stimuli (Appendix C), and 4) target stimuli used for each focus type (Appendix D). …”
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    Dataset of focus prosody in Japanese phone numbers
  20. 2780
    por Wang, Zhenyu, Wang, Lin, Zhang, Wengang
    Publicado 2019
    “…Firstly, a random angular bend (RAB) algorithm is proposed and coded in Python to simulate the geometric model of individual particle with irregular shape. …”
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    A Random Angular Bend Algorithm for Two- Dimensional Discrete Modeling of Granular Materials
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