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  1. 3701
    “…With this benchmark, we demonstrate that using auto-encoders improves the relevance of vocalisation representation which serves repertoire characterisation using a very limited number of settings. We also publish a Python package for the bioacoustic community to train their own vocalisation auto-encoders or use a pretrained encoder to browse vocal repertoires and ease unit wise annotation.…”
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    Deep audio embeddings for vocalisation clustering
  2. 3702
    “…KernelBiome is available as an open-source Python package on PyPI and at https://github.com/shimenghuang/KernelBiome.…”
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    Supervised learning and model analysis with compositional data
  3. 3703
    por Carvajal-Rodríguez, Antonio
    Publicado 2023
    “…Website implemented under the Bottle micro web-framework for Python, with all major browsers supported. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.…”
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    1LocusSim a mobile-friendly simulator for teaching population genetics
  4. 3704
    “…To facilitate the exploration and visualization of lrbi, we provide an intuitive Python notebook (Jupyter), which allows users to examine and interpret the results through various graphical representations.…”
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    MD–Ligand–Receptor: A High-Performance Computing Tool for Characterizing Ligand–Receptor Binding Interactions in Molecular Dynamics Trajectories
  5. 3705
    por Feizi, Amir, Ray, Kamalika
    Publicado 2023
    “…The portal uses GraphQL technology for efficient data query and provides endpoints for programmatic access for R and Python users. However, leveraging GraphQL for data retrieval can be challenging, time-consuming, and repetitive, requiring familiarity with the GraphQL query language and processing outputs in nested JSON (JavaScript Object Notation) format into tidy data tables. …”
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    otargen: GraphQL-based R package for tidy data accessing and processing from Open Targets Genetics
  6. 3706
    “…Here we introduce SliDL, a Python library for performing pre- and post-processing of WSIs. …”
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    SliDL: A toolbox for processing whole-slide images in deep learning
  7. 3707
    “…METHODS AND RESULTS: The GOgetter pipeline consists of bash and Python scripts. From an input FASTA file of nucleotide gene sequences, it outputs text and image files that list (1) the best hit for each input gene in a set of reference gene models, (2) all GO terms and annotations associated with those hits, and (3) a summary and visualization of GO slim categories for the data set. …”
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    GOgetter: A pipeline for summarizing and visualizing GO slim annotations for plant genetic data
  8. 3708
    “…We have made MATLAB and Python implementations of the method freely available. …”
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    insideOutside: an accessible algorithm for classifying interior and exterior points, with applications in embryology
  9. 3709
    “…Voyager is implemented in both R/Bioconductor and Python/PyPI, and features compatibility tests to ensure that both implementations return consistent results.…”
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    Voyager: exploratory single-cell genomics data analysis with geospatial statistics
  10. 3710
    “…Here, we developed a novel, publicly available, deep learning (DL)-based image analysis platform called Python-based human-in-the-loop workflow (PHILOW) implemented with a human-in-the-loop (HITL) algorithm. …”
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    An interactive deep learning-based approach reveals mitochondrial cristae topologies
  11. 3711
    “…AVAILABILITY AND IMPLEMENTATION: The scAce package is implemented in python 3.8 and is freely available from https://github.com/sldyns/scAce.…”
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    scAce: an adaptive embedding and clustering method for single-cell gene expression data
  12. 3712
    “…We have implemented this procedure in an open-source python package, MatchMaps, that can be run in any software environment supporting PHENIX and CCP4. …”
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    MatchMaps: Non-isomorphous difference maps for X-ray crystallography
  13. 3713
    por Zhang, Bao‐Lei, Guo, Xi‐Liang
    Publicado 2022
    “…Transcriptome sequencing was performed on spinal scar samples. Using Python to write code, statistical analysis and bioinformatics analysis of the correlation between transcriptome sequencing data and fiber reconstruction results are carried out. …”
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    Electroacupuncture promotes nerve regeneration and functional recovery in rats with spinal cord contusion through the coordinate interaction of CD4 and BDNF
  14. 3714
    “…Optical identification of the scratch regions and quantification were accomplished using Python code with a K-means machine-learning clustering algorithm. …”
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    Machine Learning-Enabled Quantitative Analysis of Optically Obscure Scratches on Nickel-Plated Additively Manufactured (AM) Samples
  15. 3715
    “…AVAILABILITY AND IMPLEMENTATION: P-DOR is implemented in Python3 and R and can be installed using conda environments. …”
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    P-DOR, an easy-to-use pipeline to reconstruct bacterial outbreaks using genomics
  16. 3716
    “…Therefore, this study determined trends in AAT research based on an analysis of studies published via PubMed (n = 776 studies). Python programming was used for the analysis, employing techniques such as word cloud, n-gram, two-way word tree, and CONCOR (convergence of iteration correlation) analyses. …”
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    A Text-Mining Analysis of Research Trends in Animal-Assisted Therapy
  17. 3717
    “…CHAPERONg is written in Bash and Python, and the source code is freely available at https://github.com/abeebyekeen/CHAPERONg. …”
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    CHAPERONg: A tool for automated GROMACS-based molecular dynamics simulations and trajectory analyses
  18. 3718
    “…In the current manuscript, we demonstrate a new application of the Python RecordLinkage package to family-based record linkages with machine learning algorithms for probability scoring, which we call probabilistic record linkage for families (PRLF). …”
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    An open-source probabilistic record linkage process for records with family-level information: Simulation study and applied analysis
  19. 3719
    “…AVAILABILITY AND IMPLEMENTATION: The gssnng software is available using the python package index (PyPI) and works with Scanpy AnnData objects. …”
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    Single-cell gene set scoring with nearest neighbor graph smoothed data (gssnng)
  20. 3720
    “…Here, we evaluated next-generation sequencing (NGS)-based STR profiling of human and mouse cell lines at 18 and 15 loci, respectively, in a high-throughput format. Using the Python program STRight, we demonstrate that NGS-based analysis (STR-NGS) is superior to standard STR-CE in terms of the ability to report the sequence context of repeat motifs, sensitivity and flexible multiplexing capability. …”
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    Short tandem repeat profiling via next-generation sequencing for cell line authentication
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