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  1. 3061
    “…AVAILABILITY AND IMPLEMENTATION: The details of source code are provided at http://www.robots.ox.ac.uk/~davidc/code.php. …”
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    Machine learning for classifying tuberculosis drug-resistance from DNA sequencing data
  2. 3062
    “…AVAILABILITY AND IMPLEMENTATION: Source code freely available at http://www.cs.cmu.edu/∼mxu1/software. …”
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    Deep learning-based subdivision approach for large scale macromolecules structure recovery from electron cryo tomograms
  3. 3063
    “…In this paper, a software package, hmmIBD, is introduced for estimating pairwise IBD between haploid genomes, such as those of the malaria parasite, sampled from one or two populations. Source code is freely available. METHODS: The performance of hmmIBD was verified using simulated data and benchmarked against an existing method for detecting IBD within populations. …”
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    hmmIBD: software to infer pairwise identity by descent between haploid genotypes
  4. 3064
    “…METHODS: Six organizations with established data quality assessment (DQA) programs provided documentation or source code describing current DQ checks. DQ checks were mapped to the categories within the data verification context of the harmonized DQA terminology. …”
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    A Comparison of Data Quality Assessment Checks in Six Data Sharing Networks
  5. 3065
    por Satas, Gryte, Raphael, Benjamin J
    Publicado 2018
    “…AVAILABILITY AND IMPLEMENTATION: Source code is available at https://www.github.com/raphael-group. …”
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    Haplotype phasing in single-cell DNA-sequencing data
  6. 3066
    por Nouri, Nima, Kleinstein, Steven H
    Publicado 2018
    “…AVAILABILITY AND IMPLEMENTATION: Source code for this method is freely available in the SCOPe (Spectral Clustering for clOne Partitioning) R package in the Immcantation framework: www.immcantation.org under the CC BY-SA 4.0 license. …”
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    A spectral clustering-based method for identifying clones from high-throughput B cell repertoire sequencing data
  7. 3067
    “…AVAILABILITY AND IMPLEMENTATION: The source code of CTCF-MP can be accessed at: https://github.com/ma-compbio/CTCF-MP SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.…”
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    Predicting CTCF-mediated chromatin loops using CTCF-MP
  8. 3068
    “…AVAILABILITY AND IMPLEMENTATION: The source code is available at http://www.wutbiolab.cn: 82/Gene-Phenotype-Relation-Extraction-Pipeline.zip. …”
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    A gene–phenotype relationship extraction pipeline from the biomedical literature using a representation learning approach
  9. 3069
    “…The OpenSim software is covered by the Apache License 2.0, which permits its use for any purpose including both nonprofit and commercial applications. The source code is freely and anonymously accessible on GitHub, where the community is welcomed to make contributions. …”
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    OpenSim: Simulating musculoskeletal dynamics and neuromuscular control to study human and animal movement
  10. 3070
    “…Thermodynamic analysis also suggests that site accessibility plays a role in targeting but that it cannot be used as a sole indicator for functionality. Data and source code available at: https://bitbucket.org/account/user/bipous/projects/MIRAW.…”
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    miRAW: A deep learning-based approach to predict microRNA targets by analyzing whole microRNA transcripts
  11. 3071
    por Doğan, Tunca
    Publicado 2018
    “…The datasets, results and the source code of HPO2GO are available for download at: https://github.com/cansyl/HPO2GO.…”
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    HPO2GO: prediction of human phenotype ontology term associations for proteins using cross ontology annotation co-occurrences
  12. 3072
    “…The most recent version of the source code is available at https://github.com/NIB-SI/DiNAR/ with a DOI 10.5281/zenodo.1230523 of the archived version in Zenodo. …”
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    DiNAR: revealing hidden patterns of plant signalling dynamics using Differential Network Analysis in R
  13. 3073
    “…BrownieAligner relies on multithreading to take advantage of multi-core/multi-CPU systems. The source code is available at: https://github.com/biointec/browniealigner ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-018-2319-7) contains supplementary material, which is available to authorized users.…”
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    BrownieAligner: accurate alignment of Illumina sequencing data to de Bruijn graphs
  14. 3074
    “…AVAILABILITY AND IMPLEMENTATION: The source code is available on request. The prioritized lincRNAs and their target genes are in the Supplementary Material. …”
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    CisPi: a transcriptomic score for disclosing cis-acting disease-associated lincRNAs
  15. 3075
    por Tamura, Takeyuki
    Publicado 2018
    “…CONCLUSION: We developed an efficient method for computing the design of minimum metabolic networks by using constraint-based flux balance analysis to simulate the production of useful metabolites. The source code is freely available, and is implemented in MATLAB and COBRA toolbox. …”
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    Grid-based computational methods for the design of constraint-based parsimonious chemical reaction networks to simulate metabolite production: GridProd
  16. 3076
    “…Our algorithm can be applied to any desired amplicon length without affecting computational performance. The source code of the developed algorithm is released as the mopo16S software tool (Multi-Objective Primer Optimization for 16S experiments) under the GNU General Public License and is available at http://sysbiobig.dei.unipd.it/?…”
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    Optimizing PCR primers targeting the bacterial 16S ribosomal RNA gene
  17. 3077
    “…CONCLUSIONS: DOPS is a promising meta-heuristic approach for the estimation of biochemical model parameters in relatively few function evaluations. DOPS source code is available for download under a MIT license at http://www.varnerlab.org. …”
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    Dynamic Optimization with Particle Swarms (DOPS): a meta-heuristic for parameter estimation in biochemical models
  18. 3078
    por Yang, Chia-Jung, Chiang, Jung-Hsien
    Publicado 2018
    “…By harvesting the surface names used in the training data, we wildly boosted the synonyms of GO concepts via the connection of the named concepts and then enhanced the capability to recognize more GO concepts in the text. The source code is available at https://github.com/jeroyang/ncgocr . …”
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    Gene ontology concept recognition using named concept: understanding the various presentations of the gene functions in biomedical literature
  19. 3079
    “…Overall, our results suggest that neurobiological and phenotypic biomarkers could potentially be used as an aid by the clinician, in additional to currently available clinical diagnostic standards, to improve diagnostic precision. Data and source code used in this work is publicly available at https://github.com/xinyuzhao/identification-of-brain-based-disorders.git.…”
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    Investigating the Correspondence of Clinical Diagnostic Grouping With Underlying Neurobiological and Phenotypic Clusters Using Unsupervised Machine Learning
  20. 3080
    “…SOFTWARE AVAILABILITY: The source code of aGRP can be downloaded from https://github.com/hqwang126/aGRP. …”
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    Adaptively capturing the heterogeneity of expression for cancer biomarker identification
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