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  1. 5421
    “…The benchmark dataset, intermediate results and python code which can fully reproduce our experiments and results are available at https://github.com/dqwei-lab/STS.…”
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    STS-NLSP: A Network-Based Label Space Partition Method for Predicting the Specificity of Membrane Transporter Substrates Using a Hybrid Feature of Structural and Semantic Similarity
  2. 5422
    “…RESULTS: A-Lister is a lightweight command line and graphical user interface tool written in Python. It can be executed in a differential expression mode or generic name list mode. …”
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    A-Lister: a tool for analysis of differentially expressed omics entities across multiple pairwise comparisons
  3. 5423
    “…Both workflows were implemented in the Python programming language. All code and results have been made publicly available as Jupyter notebooks on GitHub. …”
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    Migrating from partial least squares discriminant analysis to artificial neural networks: a comparison of functionally equivalent visualisation and feature contribution tools using jupyter notebooks
  4. 5424
    “…All methods are implemented in an open-source Python package, which is available at https://github.com/micom-dev/micom. …”
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    MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota
  5. 5425
    “…We developed an open-source Python-based tool—OneFL Deduper—that (1) creates seeded hash codes of combinations of patients’ quasi-identifiers using a cryptographic one-way hash function to achieve privacy protection and (2) links and deduplicates patient records using a central broker through matching of hash codes with a high precision and reasonable recall. …”
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    Implementing a hash-based privacy-preserving record linkage tool in the OneFlorida clinical research network
  6. 5426
    “…CONCLUSION: The gene expression meta-analysis and confirmation of the protein expression allow us to select five genes highly expressed PDAC samples. We could build a python script to classify the samples based on RNA expression. …”
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    PDAC-ANN: an artificial neural network to predict pancreatic ductal adenocarcinoma based on gene expression
  7. 5427
    “…METHODS: A bioinformatics analysis with Python was performed using TCGA, GEO and other databases to identify genes which are upregulated in ccRCC while being absent in the blood of healthy individuals. …”
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    Limited utility of qPCR-based detection of tumor-specific circulating mRNAs in whole blood from clear cell renal cell carcinoma patients
  8. 5428
    “…The command line interface for iREAD is implemented in Python. iREAD takes as input a BAM file, representing the transcriptome, and a text file containing the intron coordinates of a genome. …”
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    iREAD: a tool for intron retention detection from RNA-seq data
  9. 5429
    “…Linear interpolation gave the dynamic MLC aperture for the entire arc for each patient AP width category, which was subsequently applied through Python scripting. All FFF VMAT TBI plans were then evaluated by two radiation oncologists and deemed clinically acceptable. …”
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    Standardized flattening filter free volumetric modulated arc therapy plans based on anteroposterior width for total body irradiation
  10. 5430
    “…The implementation is freely available as a python library and in MetExplore webserver. METHODS: Our matching method is more flexible than an exact identifier-based correspondence since it allows establishing a link between molecules even if a different level of precision is provided in the dataset and in the metabolic network. …”
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    Improving lipid mapping in Genome Scale Metabolic Networks using ontologies
  11. 5431
    “…We used a rule-based natural language approach using a Python regex function to extract the 1) number of patients in the report, 2) clinical characteristics such as indication of the HLA testing, and 3) precise HLA genotypes. …”
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    Extracting Structured Genotype Information from Free-Text HLA Reports Using a Rule-Based Approach
  12. 5432
    “…RESULTS: CYPminer was developed in the Python language to facilitate rapid, comprehensive analysis of CYPs from genomes of all kingdoms. …”
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    CYPminer: an automated cytochrome P450 identification, classification, and data analysis tool for genome data sets across kingdoms
  13. 5433
    “…In evolutionary bioinformatics, open-source software comes in a broad range of programming languages, including C/C++, Perl, Python, Ruby, Java, and R. To avoid writing the same functionality multiple times for different languages, it is possible to share components by bridging computer languages and Bio* projects, such as BioPerl, Biopython, BioRuby, BioJava, and R/Bioconductor. …”
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    Sharing Programming Resources Between Bio* Projects
  14. 5434
    “…To support the users with various levels of programming skills, kGCN includes three interfaces: a graphical user interface (GUI) employing KNIME for users with limited programming skills such as chemists, as well as command-line and Python library interfaces for users with advanced programming skills such as cheminformaticians. …”
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    kGCN: a graph-based deep learning framework for chemical structures
  15. 5435
    “…Data were processed to identify differentially expressed miRNAs (DE-miRNAs) using the linear model in Python 3.6. Following bioinformatics analysis and reverse transcription-quantitative polymerase chain reaction validation, 8 miRNAs (miR-9-5p, miR-130a-3p, miR-92a-3p, miR-20a-5p, miR-93-5p, miR-9-3p, miR-709 and miR-124) were identified as key DE-miRNAs with low variability during mouse retinal development. …”
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    Identification of key miRNAs and genes for mouse retinal development using a linear model
  16. 5436
    “…CONCLUSIONS: Keras R-CNN is a Python package that performs automated cell identification for both brightfield and fluorescence images and can process large image sets. …”
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    Keras R-CNN: library for cell detection in biological images using deep neural networks
  17. 5437
    “…At the US Arid Land Agricultural Center in Maricopa Arizona, USA a data workflow was developed for a terrestrial FB-HTPP platform that utilized a custom Python application and a PostgreSQL database. The workflow developed for the HTPP platform enables users to capture and organize data and verify data quality before statistical analysis. …”
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    A data workflow to support plant breeding decisions from a terrestrial field-based high-throughput plant phenotyping system
  18. 5438
    “…Basic demographic and comparative analysis were performed using the Python3.8.2 software (Windows 10 64 bit, USA). RESULTS: Amongst all the states of India most respondents hailed from the top ten affected states. …”
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    “Compliance of the Indian National Task Force guidelines for COVID-19 recommendation by Indian doctors – A survey"
  19. 5439
    “…AlbaTraDIS is written in Python 3 and is available under the open source licence GNU GPL 3 from https://github.com/quadram-institute-bioscience/albatradis.…”
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    AlbaTraDIS: Comparative analysis of large datasets from parallel transposon mutagenesis experiments
  20. 5440
    “…We, therefore, developed a Python tool to automatically extract, process, and categorize open-access articles published from January 1, 1987 to October 1, 2019 in the PubMed, PubMed Central, JSTOR, Paperity, and arXiV databases. …”
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    Social, Behavioral, and Cultural factors of HIV in Malawi: Semi-Automated Systematic Review
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