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  1. 3221
    “…The PHG Docker used to generate the simulation results is https://hub.docker.com/ as maizegenetics/phg:0.0.27. PHG source code is at https://bitbucket.org/bucklerlab/practicalhaplotypegraph/src/master/. …”
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    The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation
  2. 3222
    “…This allows e.g. accurate marker filtering ahead of data analysis. CONCLUSIONS: The source code (Python version 3.9.4), a standalone executive file, and example data for ImputAccur are freely available at https://gitlab.gwdg.de/kolja.thormann1/imputationquality.git. …”
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    ImputAccur: fast and user-friendly calculation of genotype-imputation accuracy-measures
  3. 3223
    “…FindPFΔS is freely available as both Python source code on GitHub (https://github.com/JonZwe/FindPFAS) and as an executable windows application (https://doi.org/10.5281/zenodo.6797353) with a graphical user interface on Zenodo.…”
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    FindPFΔS: Non-Target Screening for PFAS—Comprehensive Data Mining for MS(2) Fragment Mass Differences
  4. 3224
    “…Although developed during the COVID-19 pandemic, it allows easy annotation of any data as they are consumed by analyses, or conversely traces the provenance of scientific outputs back through the analytical or modelling source code to primary data. Such a tool provides a mechanism for the public, and fellow scientists, to better assess scientific evidence by inspecting its provenance, while allowing scientists to support policymakers in openly justifying their decisions. …”
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    FAIR data pipeline: provenance-driven data management for traceable scientific workflows
  5. 3225
    “…The web service is freely accessible through URL: https://biolearns.medicine.iu.edu/. Source code is available at https://github.com/huangzhii/TSUNAMI/.…”
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    TSUNAMI: Translational Bioinformatics Tool Suite for Network Analysis and Mining
  6. 3226
    “…To comply with the FAIR (Findable, Accessible, Interoperable and Reusable) principle, the source code and documentation of the toolbox have been made available via an open-access repository.…”
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    ABOT: an open-source online benchmarking tool for machine learning-based artefact detection and removal methods from neuronal signals
  7. 3227
    “…We had full access to source code, comments on code, change requests, test reports, every deliverable (60 in total) produced for the software certification (safety concepts, requirements specifications, architecture and design, testing activities, etc.), notes, whiteboard sketches, emails, etc. …”
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    Guidelines for the development of a critical software under emergency
  8. 3228
    “…Of these records, 135,542 preserve the page’s source code, 258,416 have the attack target brand detected, 70,597 have the hosting service identified, and 15,008 have the shortener service discovered. …”
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    Piracema: a Phishing snapshot database for building dataset features
  9. 3229
    “…The current study's source code is available to the research community at https://github.com/csbioinfopk/enpred.…”
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    A machine learning technique for identifying DNA enhancer regions utilizing CIS-regulatory element patterns
  10. 3230
    “…Gnocis can be installed using the PyPI package manager by running ‘pip install gnocis’. The source code is available on GitHub, at https://github.com/bjornbredesen/gnocis.…”
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    Gnocis: An integrated system for interactive and reproducible analysis and modelling of cis-regulatory elements in Python 3
  11. 3231
    “…Tag data from humpback and beluga whales were then used to demonstrate how the gait analysis can be used to enhance tag-based investigations of movement and behavior. The MATLAB source code and data presented in the paper are publicly available (https://github.com/ding-z/cetacean-pose-gait-analysis.git), along with suggested best practices.…”
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    Pose-gait analysis for cetacean biologging tag data
  12. 3232
    “…AVAILABILITY AND IMPLEMENTATION: The source code is freely available at https://github.com/JieZheng-ShanghaiTech/HiCoEx. …”
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    Prediction of gene co-expression from chromatin contacts with graph attention network
  13. 3233
    “…Our network analysis reveals a fast recovery of the infected cohort after the second IAV infection and provides insights into crucial roles of Desulfovibrionaceae and Lactobacillaceae families in combating Influenza A Virus infection. Source code of the community detection algorithm can be downloaded from https://github.com/AniBhar84/MCCD-WN.…”
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    Application of a maximal-clique based community detection algorithm to gut microbiome data reveals driver microbes during influenza A virus infection
  14. 3234
    “…On the whole, TranGRU achieves better performance for molecular property prediction. The source code is available in GitHub: https://github.com/Jiangjing0122/TranGRU.…”
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    TranGRU: focusing on both the local and global information of molecules for molecular property prediction
  15. 3235
    “…The Bioregistry can be accessed through https://bioregistry.io and its source code and data are available under the MIT and CC0 Licenses at https://github.com/biopragmatics/bioregistry.…”
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    Unifying the identification of biomedical entities with the Bioregistry
  16. 3236
    “…This technical guide is supported by a step-by-step computational tutorial accessible under https://tritexassembly.bitbucket.io/. The TRITEX source code is hosted under this URL: https://bitbucket.org/tritexassembly. …”
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    A technical guide to TRITEX, a computational pipeline for chromosome-scale sequence assembly of plant genomes
  17. 3237
    “…Finally, parallel scaling up to 64 processes in the open-source code Force Field X is presented.…”
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    Progressive alignment of crystals: reproducible and efficient assessment of crystal structure similarity
  18. 3238
    “…VIBE is a powerful, free, open source and locally installable solution for prioritizing genes based on patient symptoms. Project source code, documentation, benchmark and executables are available at https://github.com/molgenis/vibe.…”
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    A pipeline‐friendly software tool for genome diagnostics to prioritize genes by matching patient symptoms to literature
  19. 3239
    “…These statistics suggest that our method has surpassed the existing state-of-the-art methods on the COVIDx CT-2A dataset. Source code is available at https://github.com/YujiaKCL/COVID-CT-Similarity-Regularization.…”
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    Improving COVID-19 CT classification of CNNs by learning parameter-efficient representation
  20. 3240
    “…We make CerebNet available as source-code (https://github.com/Deep-MI/FastSurfer).…”
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    CerebNet: A fast and reliable deep-learning pipeline for detailed cerebellum sub-segmentation
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