“…In addition to type IV effector prediction, we believe that the proposed framework can provide instructive guidance for similar studies to construct prediction methods on related biological problems. The data and source code of this study can be freely accessed at https://github.com/CT001002/T4SE-XGB.…”
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“…To accelerate the investigation of protein ubiquitylation, the data sets and source code used in this study are freely available at https://github.com/wang-hong-fei/DL-plant-ubsites-prediction.…”
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“…PyOIF is based on Python objects representing the cells and on the C++ computational core for fluid and interaction dynamics. The source code is freely available at GitHub repository, runs natively under Linux and MacOS and can be used in Windows Subsystem for Linux. …”
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“…Our results demonstrate that seekCRIT is a novel and efficient approach to detect DECs using rRNA depleted RNA-seq data. seekCRIT is freely downloadable at https://github.com/UofLBioinformatics/seekCRIT. The source code is licensed under the MIT License. seekCRIT is developed and tested on Linux CentOS-7.…”
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“…NAguideR is freely available at http://www.omicsolution.org/wukong/NAguideR/ and the source code: https://github.com/wangshisheng/NAguideR/.…”
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“…The DEEPScreen system can be exploited in the fields of drug discovery and repurposing for in silico screening of the chemogenomic space, to provide novel DTIs which can be experimentally pursued. The source code, trained "ready-to-use" prediction models, all datasets and the results of this study are available at ; https://github.com/cansyl/DEEPscreen.…”
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“…Its distributed storage and distributed computation technique allow us to efficiently analyze large-scale single-cell data at the cost of constant time speedup. The source code for D-EE algorithm based on C and MPI tailored to a high-performance computing cluster is available at https://github.com/ShaokunAn/D-EE.…”
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“…Subsequently, we detected cancer-related significantly enriched gene ontology terms and pathways, probable drug targets, two co-expressed modules associated significantly with several clinical features, such as number of positive lymph nodes, Nottingham prognostic index, and tumor stage, and two biologically distinct groups of BRCA patients. Data and source code of the case study can be downloaded at https://github.com/hauldhut/drivergene.…”
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“…AVAILABILITY AND IMPLEMENTATION: LDMF is freely available online at www.cbrc.kaust.edu.sa/ldmf; Source code is available at https://github.com/tanviralambd/LD/. …”
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“…Finally, we release our data and source code to support standardization efforts in OCTA image segmentation. …”
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“…AVAILABILITY AND IMPLEMENTATION: Source code is freely available within Metabolomics toolbox GitHub repository (https://github.com/artedison/Edison_Lab_Shared_Metabolomics_UGA/tree/master/metabolomics_toolbox/code/ridge_tracking) and is implemented in MATLAB and R. …”
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“…The 3D structures of the X-chromosome at 3 hours, 6 hours, and 24 hours after the start of the Xist expression, which initiates the XCI process, have been reconstructed. The source code and the reconstructed 3D structures of the X-chromosome can be downloaded from http://dna.cs.miami.edu/3D-XCI/.…”
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“…We provide DeepImmuno-CNN as source code and an easy-to-use web interface.…”
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“…The tool can accessed from: http://genomics.lshtm.ac.uk/immuno (online); https://github.com/dan-ward-bio/COVID-immunoanalytics (source code).…”
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“…DeCban outperforms the mainstream deep learning-based methods on not only prediction accuracy but also computational efficiency. The data sets and source code of this study are freely available at: https://github.com/AaronYll/DECban.…”
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“…HOPE's basic idea is suitable for other related scenarios, such as the prediction of gene function based on gene co-expression networks. The source code of HOPE is freely available at https://github.com/adrift00/HOPE.…”
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“…The GCA R package is available at GitHub and the source code is provided as open source. CONCLUSIONS: The GCA R package allows users to easily assess the connectedness of their data. …”
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“…PrecocityDB is freely accessible at http://www.precocity.bicnirrh.res.in. The database source code and content can be downloaded through GitHub (https://github.com/bic-nirrh/precocity).…”
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“…From data from 20 triple-negative breast cancer patients, our approaches effectively prioritize genes that are essential for breast cancer cell fitness and predict patient survival, including those implicating convergent evolution. The source code of our study is available at https://github.com/KChen-lab/MEDALT. …”
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“…The domain language fuels a template-based code generator, allowing the generation of the dashboards’ source code. Applying domain engineering to the dashboards’ domain improves the development and maintainability of these complex software products given the variety of requirements that users might have regarding their graphical interfaces.…”
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