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  1. 2681
    “…This modular approach is based on open-source code and allows researchers to customise and further develop the presented functionalities to various types of data and questions related to analysis of marine imagery. …”
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    An open-source, citizen science and machine learning approach to analyse subsea movies
  2. 2682
    “…We discuss the multiple use cases Flype supports such as (a) in‐house NGS tests, (b) in‐house pharmacogenomics (PGX) tests, (c) dramatic scale‐up of genomic testing using an external lab, (d) consumer genomics using two external partners, and (e) a variety of reporting tools. The source code for Flype is available upon request to the authors.…”
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    Flype: Software for enabling personalized medicine
  3. 2683
    “…However, most sentence similarity methods and experimental results reported in the biomedical domain cannot be reproduced for multiple reasons as follows: the copying of previous results without confirmation, the lack of source code and data to replicate both methods and experiments, and the lack of a detailed definition of the experimental setup, among others. …”
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    Protocol for a reproducible experimental survey on biomedical sentence similarity
  4. 2684
    “…AVAILABILITY AND IMPLEMENTATION: The source code of this work is available at https://github.com/weberlab-hhu/Helixer under the GNU General Public License v3.0. …”
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    Helixer: cross-species gene annotation of large eukaryotic genomes using deep learning
  5. 2685
    “…Simulation results are produced to demonstrate the mobility and handover capabilities, and the performance gains from the LiFi-WiFi hybrid system in terms of packet delay, throughput, packet drop ratio (PDR), and fairness between users. The source code of the framework is made available for the use of the research community.…”
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    A Comprehensive Open-Source Simulation Framework for LiFi Communication
  6. 2686
    “…AVAILABILITY AND IMPLEMENTATION: The source code is available at https://github.com/rajinder4489/FuSe. …”
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    FuSe: a tool to move RNA-Seq analyses from chromosomal/gene loci to functional grouping of mRNA transcripts
  7. 2687
    “…Moreover, we assessed the biological relevance of one LRE discovered by DExTER in P. falciparum using an in vivo reporter assay. The source code (python) of DExTER is available at https://gite.lirmm.fr/menichelli/DExTER.…”
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    Identification of long regulatory elements in the genome of Plasmodium falciparum and other eukaryotes
  8. 2688
    “…AVAILABILITY AND IMPLEMENTATION: Our method is available as a Python package at https://github.com/jmschrei/kiwano and can be installed using the command pip install kiwano. The source code used here and the similarity matrix can be found at http://doi.org/10.5281/zenodo.3708538. …”
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    Prioritizing transcriptomic and epigenomic experiments using an optimization strategy that leverages imputed data
  9. 2689
    “…Our analysis shows that (1) logging is challenging not only in open-source projects but also in industry, (2) machine learning is a promising approach to enable a contextual analysis of source code for log recommendation but further investigation is required to assess the usability of those tools in practice, (3) few studies approached efficient persistence of log data, and (4) there are open opportunities to analyze application logs and to evaluate state-of-the-art log analysis techniques in a DevOps context.…”
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    Log-based software monitoring: a systematic mapping study
  10. 2690
    “…Crinet-inferred ceRNA groups that were consistently involved in the immune system related processes could be important assets in the light of the studies confirming the relation between immunotherapy and cancer. The source code of Crinet is in R and available at https://github.com/bozdaglab/crinet.…”
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    Crinet: A computational tool to infer genome-wide competing endogenous RNA (ceRNA) interactions
  11. 2691
    “…Moreover, the significant alternative splicing events identified by AS-Quant between two biological contexts were validated by RT-PCR experiment. (3) Availability: AS-Quant is implemented in Python 3.0. Source code and a comprehensive user’s manual are freely available online.…”
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    AS-Quant: Detection and Visualization of Alternative Splicing Events with RNA-seq Data
  12. 2692
    “…SUMMARY: ViBiBa, which is a highly flexible tool that allows for decentralized sample storage of liquid biopsy specimens, facilitates a solution which promotes collaboration in a user-friendly, federalist and highly structured way. The source code is available under the MIT license from https://vibiba.com or https://github.com/asperciesl/ViBiBa…”
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    ViBiBa: Virtual BioBanking for the DETECT multicenter trial program - decentralized storage and processing
  13. 2693
    “…On the A101 dataset, our predictor outperformed 1.34% (accuracy), 0.0227 (Matthew’s correlation coefficient), 5.63% (specificity), and 0.0081 (AUC) than comparing predictors, which indicates that m6AGE is a useful tool for m(6)A site prediction. The source code of m6AGE is available at https://github.com/bokunoBike/m6AGE.…”
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    m6AGE: A Predictor for N6-Methyladenosine Sites Identification Utilizing Sequence Characteristics and Graph Embedding-Based Geometrical Information
  14. 2694
    “…From our experimental results, we found that CatBoost yielded the highest accuracy (92.55%), which is at par with other state-of-the-art results—most of which employ Deep Learning architectures. The source code is available in the GitHub repository.…”
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    Computer Aided Breast Cancer Detection Using Ensembling of Texture and Statistical Image Features
  15. 2695
    por Deng, Lei, Wu, Hui, Liu, Xuejun, Liu, Hui
    Publicado 2021
    “…Moreover, we verify that the performance of DeepD2V using word2vec-based k-mer distributed representation is better than one-hot encoding, and the integrated framework of both convolutional neural network (CNN) and bidirectional LSTM (bi-LSTM) outperforms CNN or the bi-LSTM model when used alone. The source code of DeepD2V is available at the github repository.…”
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    DeepD2V: A Novel Deep Learning-Based Framework for Predicting Transcription Factor Binding Sites from Combined DNA Sequence
  16. 2696
    “…Especially in complex statistical analyses—such as the analysis of longitudinal data—reproducing results is far from simple, especially if no source code is available. In this work we aimed to reproduce analyses of longitudinal data of 11 articles published in PLOS ONE. …”
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    A computational reproducibility study of PLOS ONE articles featuring longitudinal data analyses
  17. 2697
    “…All data used in the experiments as well as our source code are freely available. We demonstrate its usefulness within an existing larger scaffolding approach by solving realistic instances resulting from partial Arabidopsis thaliana assemblies in short computation time.…”
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    Using the longest run subsequence problem within homology-based scaffolding
  18. 2698
    “…RENET2 is an efficient and accurate method for full-text gene–disease association extraction. The source-code, manually curated abstract/full-text training data, and results of RENET2 are available at GitHub.…”
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    RENET2: high-performance full-text gene–disease relation extraction with iterative training data expansion
  19. 2699
    “…For an easier local run, it also provides a prebuilt Docker image that requires no installation, as a supplementary to the source code version. KOBAS can be freely accessed at http://kobas.cbi.pku.edu.cn, and a mirror site is available at http://bioinfo.org/kobas.…”
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    KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis
  20. 2700
    por Trinh, Hung-Cuong, Kwon, Yung-Keun
    Publicado 2021
    “…AVAILABILITY AND IMPLEMENTATION: Source code and data are freely available at https://github.com/csclab/CGA-BNI. …”
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    A novel constrained genetic algorithm-based Boolean network inference method from steady-state gene expression data
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