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  1. 5081
    “…To address this fact, we present Diffusion Microstructure Imaging in Python (Dmipy), an open-source toolbox implementing PGSE-based MC-modeling in its most general form. …”
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    The Dmipy Toolbox: Diffusion MRI Multi-Compartment Modeling and Microstructure Recovery Made Easy
  2. 5082
    “…AVAILABILITY AND IMPLEMENTATION: multiPhATE was implemented in Python 3.7, and runs as a command-line code under Linux or Unix. multiPhATE is freely available under an open-source BSD3 license from https://github.com/carolzhou/multiPhATE. …”
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    multiPhATE: bioinformatics pipeline for functional annotation of phage isolates
  3. 5083
    “…All the C++ source code and python scripts utilized in this study can be downloaded on the Internet (https://github.com/qkirikigaku/MS_LDA). …”
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    Discovering novel mutation signatures by latent Dirichlet allocation with variational Bayes inference
  4. 5084
    “…The algorithms were implemented in the Python programming language. All code and results have been made publicly available as Jupyter notebooks. …”
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    A comparative evaluation of the generalised predictive ability of eight machine learning algorithms across ten clinical metabolomics data sets for binary classification
  5. 5085
    “…These can be queried using Python, R, Java, and MATLAB, for data-driven optoelectronic materials discovery.…”
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    Comparative dataset of experimental and computational attributes of UV/vis absorption spectra
  6. 5086
    “…Our method makes a valuable contribution towards minimising genotyping errors and reducing costs associated with developing a novel marker panel. The Python script to perform our method of multi‐individual microsatellite identification (MiMi) is freely available from GitHub (https://github.com/graemefox/mimi).…”
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    Multi‐individual microsatellite identification: A multiple genome approach to microsatellite design (MiMi)
  7. 5087
    “…By following these example workflows, users can benefit from CNN-based segmentation without possessing knowledge of Python programming or CNN frameworks.…”
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    UNI-EM: An Environment for Deep Neural Network-Based Automated Segmentation of Neuronal Electron Microscopic Images
  8. 5088
    “…AVAILABILITY AND IMPLEMENTATION: Weighted edge network analysis (WENA) data and source codes for performing spectral decomposition of the signal (SDS) and WENA analysis, both written using Python, are available at http://www.broca.inserm.fr/HD-WENA/. …”
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    Genetic cooperativity in multi-layer networks implicates cell survival and senescence in the striatum of Huntington’s disease mice synchronous to symptoms
  9. 5089
    “…The greedy weighting algorithm has a variety of possible applications and is fast and efficient. A python implementation is provided.…”
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    A greedy stacking algorithm for model ensembling and domain weighting
  10. 5090
    “…AVAILABILITY AND IMPLEMENTATION: Crossmapper is a command line tool implemented in Python 3.6 and available as a conda package, allowing effortless installation. …”
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    CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies
  11. 5091
    “…CONCLUSIONS: The GenomeQC web application is implemented in R/Shiny version 1.5.9 and Python 3.6 and is freely available at https://genomeqc.maizegdb.org/ under the GPL license. …”
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    GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations
  12. 5092
    “…We provide code to analyze and export/import stimuli, behavior, and electrophysiological recordings to/from NWB in both MATLAB and Python. The data files are NWB:N compliant, which affords interoperability between programming languages and operating systems. …”
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    A NWB-based dataset and processing pipeline of human single-neuron activity during a declarative memory task
  13. 5093
    “…CONCLUSIONS: We combine an error correction strategy with a number of algorithmic improvements in a new version of the duplex analysis software, Du Novo 2.0. It is written in Python, C, AWK, and Bash. It is open source and readily available through Galaxy, Bioconda, and Github: https://github.com/galaxyproject/dunovo.…”
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    Family reunion via error correction: an efficient analysis of duplex sequencing data
  14. 5094
    por Zhang, Jianbo, Panthee, Dilip R.
    Publicado 2020
    “…RESULTS: We developed a simple and effective algorithm for BSA-Seq data analysis and implemented it in Python; the program was named PyBSASeq. Using PyBSASeq, the significant SNPs (sSNPs), SNPs likely associated with the trait, were identified via Fisher’s exact test, and then the ratio of the sSNPs to total SNPs in a chromosomal interval was used to detect the genomic regions that condition the trait of interest. …”
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    PyBSASeq: a simple and effective algorithm for bulked segregant analysis with whole-genome sequencing data
  15. 5095
    “…RESULTS: We developed a command line interface python package, pyCancerSig, to perform sample profiling by integrating single nucleotide variation (SNV), structural variation (SV) and microsatellite instability (MSI) profiles into a unified profile. …”
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    pyCancerSig: subclassifying human cancer with comprehensive single nucleotide, structural and microsatellite mutational signature deconstruction from whole genome sequencing
  16. 5096
    “…The current BioModels platform allows submission of models encoded in diverse modelling formats, including SBML, CellML, PharmML, COMBINE archive, MATLAB, Mathematica, R, Python or C++. The models submitted to BioModels are curated to verify the computational representation of the biological process and the reproducibility of the simulation results in the reference publication. …”
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    BioModels—15 years of sharing computational models in life science
  17. 5097
    “…Seeds were loaded into the system and all seeds in a sample were automatically individually imaged to acquire top and side views as they passed through an imaging chamber. A Python analysis script applied a colour calibration and extracted quantifiable traits of seed colour, size and shape. …”
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    The BELT and phenoSEED platforms: shape and colour phenotyping of seed samples
  18. 5098
    por Magnusson, Rasmus, Gustafsson, Mika
    Publicado 2020
    “…AVAILABILITY AND IMPLEMENTATION: We made LiPLike available to the community as a Python toolbox, available at https://gitlab.com/Gustafsson-lab/liplike. …”
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    LiPLike: towards gene regulatory network predictions of high certainty
  19. 5099
    “…RESULTS: The open-source python program YSMR (Your Software for Motility Recognition) was designed to simultaneously track a large number of bacterial cells on standard computers from video files in various formats. …”
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    YSMR: a video tracking and analysis program for bacterial motility
  20. 5100
    “…Data processing and statistical analyses were performed in mothur, Python, R, and SAS. RESULTS: Of 696 participants, urinary Pb concentration was highest in those age 70 +, females, those with a high school diploma or lower, current and former smokers, and those without indoor pets. …”
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    Urinary lead concentration and composition of the adult gut microbiota in a cross-sectional population-based sample
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