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  1. 3201
    “…We have released the source code at https://github.com/JerRuy/Pyramid-Net.…”
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    Pyramid-Net: Intra-layer Pyramid-Scale Feature Aggregation Network for Retinal Vessel Segmentation
  2. 3202
    por Xu, Gang, Wang, Qinghua, Ma, Jianpeng
    Publicado 2021
    “…OPUS-Fold2 is written in Python and TensorFlow2.4, which is user-friendly to any source-code-level modification. AVAILABILITYAND IMPLEMENTATION: The code and pre-trained models of OPUS-X can be downloaded from https://github.com/OPUS-MaLab/opus_x. …”
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    OPUS-X: an open-source toolkit for protein torsion angles, secondary structure, solvent accessibility, contact map predictions and 3D folding
  3. 3203
    por He, Di, Xie, Lei
    Publicado 2021
    “…AVAILABILITYAND IMPLEMENTATION: The source code is freely available at https://github.com/XieResearchGroup/CLEIT. …”
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    A cross-level information transmission network for hierarchical omics data integration and phenotype prediction from a new genotype
  4. 3204
    “…To that end, there is no registration required to download the source code or runtime code for the ICE service and its default rule. …”
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    Immunization calculation engine: An open source immunization evaluation and forecasting system
  5. 3205
    “…The proposed method performs better results compared to the state-of-the-art learning to augment strategies in terms of sensitivity (0.808), specificity (0.915), and F-Measure (0.737). The source code of the proposed method is available at https://github.com/mohamadmomeny/Learning-to-augment-strategy.…”
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    Learning-to-augment strategy using noisy and denoised data: Improving generalizability of deep CNN for the detection of COVID-19 in X-ray images
  6. 3206
    “…AVAILABILITY AND IMPLEMENTATION: VaLiAnT is a command line tool written in Python. Source code, testing data, example input and output files and executables are available (https://github.com/cancerit/VaLiAnT) in addition to a detailed user manual (https://github.com/cancerit/VaLiAnT/wiki). …”
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    Variant Library Annotation Tool (VaLiAnT): an oligonucleotide library design and annotation tool for saturation genome editing and other deep mutational scanning experiments
  7. 3207
    “…We suggest that the flexible design idea of CITEMO can be an inspiration for other single-cell multimodal tasks. The complete source code and dataset of the CITEMO framework can be obtained from https://github.com/studentiz/CITEMO.…”
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    CITEMO(XMBD): A flexible single-cell multimodal omics analysis framework to reveal the heterogeneity of immune cells
  8. 3208
    “…Our comprehensive evaluation using 25 publicly available scRNA-seq datasets and various simulation scenarios against five state-of-the-art methods demonstrates that scISR is better than other imputation methods in recovering scRNA-seq expression profiles via imputation. scISR consistently improves the quality of cluster analysis regardless of dropout rates, normalization techniques, and quantification schemes. The source code of scISR can be found on GitHub at https://github.com/duct317/scISR.…”
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    A novel method for single-cell data imputation using subspace regression
  9. 3209
    “…AVAILABILITY: The exposomeShiny source code is freely available on Github at [https://github.com/isglobal-brge/exposomeShiny], Git tag v1.4. …”
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    Software Application Profile: exposomeShiny—a toolbox for exposome data analysis
  10. 3210
    “…Code smells are poor implementation choices that developers apply while evolving source code and that affect program maintainability. …”
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    On the adequacy of static analysis warnings with respect to code smell prediction
  11. 3211
    “…CONCLUSIONS: Semantic type prediction is a key part of building accurate NLP pipelines for broad-coverage information extraction from biomedical text. We make our source code and novel datasets publicly available to foster reproducible research.…”
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    Improving broad-coverage medical entity linking with semantic type prediction and large-scale datasets
  12. 3212
    “…AVAILABILITY AND IMPLEMENTATION: Source code and datasets are available at https://github.com/ibivu/pipenn/. …”
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    PIPENN: protein interface prediction from sequence with an ensemble of neural nets
  13. 3213
    “…Therefore, this framework has a great potential to be used in clinical and telehealth applications. The source code is available at https://github.com/sdnjly/WSDL-AD.…”
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    Generalizable Beat-by-Beat Arrhythmia Detection by Using Weakly Supervised Deep Learning
  14. 3214
    por Feng, Xikang, Chen, Lingxi
    Publicado 2022
    “…CONCLUSIONS: SCSilicon is a user-friendly software package for users to develop and benchmark single-cell CNV callers. Source code of SCSilicon is available at https://github.com/xikanfeng2/SCSilicon. …”
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    SCSilicon: a tool for synthetic single-cell DNA sequencing data generation
  15. 3215
    “…AVAILABILITY AND IMPLEMENTATION: HPiP is released as an open-source code under the MIT license that is freely available on GitHub (https://github.com/BabuLab-UofR/HPiP) as well as on Bioconductor (http://bioconductor.org/packages/devel/bioc/html/HPiP.html). …”
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    HPiP: an R/Bioconductor package for predicting host–pathogen protein–protein interactions from protein sequences using ensemble machine learning approach
  16. 3216
    “…The refgenie Data Manager tool can be installed via the Galaxy ToolShed, with source code managed at https://github.com/BlankenbergLab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull and released using an MIT license. …”
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    Expanding the Galaxy’s reference data
  17. 3217
    “…The simulation results demonstrate that the CO algorithm can successfully solve large-scale and challenging optimization problems and offers a significant advantage over different standards and improved and hybrid existing algorithms. Note that the source code of the CO algorithm is publicly available at https://www.optim-app.com/projects/co.…”
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    The cheetah optimizer: a nature-inspired metaheuristic algorithm for large-scale optimization problems
  18. 3218
    “…Our model is flexible to configure and simple to modify for modeling different scenarios under different environmental conditions and mitigation measures. We release the source code of the COVIDHunter implementation at https://github.com/CMU-SAFARI/COVIDHunter and show how to flexibly configure our model for any scenario and easily extend it for different measures and conditions than we account for.…”
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    COVIDHunter: COVID-19 Pandemic Wave Prediction and Mitigation via Seasonality Aware Modeling
  19. 3219
    “…Additionally, a GitHub link (https://github.com/sanjaysinghrathi/DILI-Classifier) for app source code and ISMB extended video talk (https://www.youtube.com/watch?…”
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    DILI( C ): An AI-Based Classifier to Search for Drug-Induced Liver Injury Literature
  20. 3220
    “…CONCLUSION: The proposed methods simplify inter‐scan motion correction of [Formula: see text] maps and are applicable at both 3T and 7T, where a body coil is typically not available. The open‐source code for all methods is made publicly available.…”
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    Correcting inter‐scan motion artifacts in quantitative R (1) mapping at 7T
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