“…To the best of our knowledge, ASGAL is the first tool that detects novel alternative splicing events by directly aligning reads to a splicing graph. AVAILABILITY: Source code, documentation, and data are available for download at http://asgal.algolab.eu.…”
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“…AVAILABILITY AND IMPLEMENTATION: Source code for the LSTM-CRF is available at https://github.com/Franck-Dernoncourt/NeuroNER/ and links to the corpora are available at https://github.com/BaderLab/Transfer-Learning-BNER-Bioinformatics-2018/. …”
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“…These lists indicate that human action has a major impact on lake microbiomes. SEDE-GPS and its source code is available for download at http://SEDE-GPS.heiderlab.de ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-018-2419-4) contains supplementary material, which is available to authorized users.…”
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“…Using motif detection with the learned filters, not only important known structures (motifs) such as protein-binding sites but also structures of unknown functional groups were detected. CONCLUSIONS: The source code of our SMILES-based convolutional neural network software in the deep learning framework Chainer is available at http://www.dna.bio.keio.ac.jp/smiles/, and the dataset used for performance evaluation in this work is available at the same URL.…”
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“…The advantages of k-dominating set variable selection were also illustrated in two applications: pedigree reconstruction using SNP profiles of 1,372 Douglas-fir trees, and species delineation for 226 grasshopper mouse samples. A C++ source code that implements SNP-SELECT and uses Gurobi optimization solver for the k-dominating set variable selection is available (https://github.com/transgenomicsosu/SNP-SELECT).…”
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“…AVAILABILITY AND IMPLEMENTATION: CIRCOAST source code available at: https://github.com/uva-peirce-cottler-lab/ARCAS. …”
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“…CONCLUSION: WGDdetector is not only reliable and stable for genome data, but also a new way to using the transcriptome data to obtain the correct dS distribution for detecting WGD. The source code is freely available, and is implemented in Windows and Linux operation system. …”
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“…The signal processing method, MLBP, thus offers a viable alternative feature space to textual representations of sequence data. The source code for our Multi-resolution Genomic Binary Patterns method can be found at https://github.com/skouchaki/MrGBP.…”
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“…For convenience, svist4get is provided as pypi package. The source code is available at https://bitbucket.org/artegorov/svist4get/ ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-019-2706-8) contains supplementary material, which is available to authorized users.…”
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“…The IPCT web and the source code are available in Sample Availability section.…”
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“…Our study shows the feasibility of discovering breast cancer related co-expression modules, sketch a blueprint of future endeavors on Deep Learning-based survival analysis. SALMON source code is available at https://github.com/huangzhii/SALMON/.…”
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“…The NOJAH application tool is available at http://bbisr.shinyapps.winship.emory.edu/NOJAH/ http://shinygispa.winship.emory.edu/shinyGISPA/ with corresponding source code available at https://github.com/bbisr-shinyapps/NOJAH/.…”
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“…The extended CGBayesNets package is freely available under the MIT Open Source license agreement. The source code and documentation can be downloaded from https://github.com/jlugomar/longitudinal_microbiome_analysis_public. …”
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“…The results show that scNBMF is a more powerful tool in large-scale scRNAseq data analysis. scNBMF was implemented in R and Python, and the source code are freely available at https://github.com/sqsun.…”
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“…Recentrifuge’s official website is www.recentrifuge.org. The data and source code are anonymously and freely available on GitHub and PyPI. …”
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“…This suggested that the LocNuclei predictions carry important information about function. The source code and data sets are available through GitHub: https://github.com/Rostlab/LocNuclei. …”
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“…CONCLUSIONS: SpliceV is an easy-to-use splicing visualization tool, compatible with both Python 2.7 and 3+, and distributed under the GNU Public License. The source code is freely available for download at https://github.com/flemingtonlab/SpliceV and can be installed from PyPI using pip. …”
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“…The neural network architecture of DEEPred can also be applied to the prediction of the other types of ontological associations. The source code and all datasets used in this study are available at: https://github.com/cansyl/DEEPred.…”
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“…CONCLUSIONS: The final results imply that driver genes are those prone to have higher variation frequency and impact more dysregulated genes in the common significant compartment. AVAILABILITY: The source code can be obtained at https://github.com/weiba/Subdyquency. …”
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“…The O3D open services can allow cognitive and clinical neuroscientists to run the connectome mapping algorithms on new, user-uploaded, data. Open source code implementing all O3D services is also provided to allow computational and computer scientists to reuse and extend the processing methods. …”
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