“…Third, most of the existing DGFs need the source code of the test programs, which is not available for binary programs. …”
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“…More specifically, it combines a whole sequence-based XGBoost model and an N-terminal sequence-based convolutional neural network model; 5-fold cross-validation and independent tests demonstrate that ASPIRER achieves superior performance than existing state-of-the-art approaches. The source code and curated datasets of ASPIRER are publicly available at https://github.com/yanwu20/ASPIRER/. …”
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“…We further illustrated through several case studies how the improved computational efficiency enables more sophisticated tracking models and yields better tracking accuracy. We made the source code publicly available on GitHub with both Python and MATLAB interfaces.…”
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“…Another encouraging observation is that the network information can significantly boost the predictive performance of sequence-based method. All source code and dataset of SGII have been deposited in a GitHub repository (https://github.com/ninglolo/SGII).…”
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“…In conclusion, the MutCov is of high importance for systematically evaluating the effect of novel mutations and improving the prevention and treatment of COVID-19. The source code and installation instruction of MutCov are freely available at http://jianglab.org.cn/MutCov.…”
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“…AVAILABILITY AND IMPLEMENTATION: The source code for SmMIP-tools, its manual and additional scripts aimed to foster large-scale data processing and analysis are all available on github (https://github.com/abelson-lab/smMIP-tools). …”
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“…AVAILABILITY AND IMPLEMENTATION: Source code and binaries are freely available for download at URL: https://github.com/Chenlab-UMN/Ub-E3-ligase-Activity-Profiling-Analysis, implemented in python and supported on Linux and MS Windows. …”
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“…Benchmarks against existing tools clearly demonstrate the need for FRET-IBRA in extracting reliable insights from FRET microscopy images of dynamic physiological processes at high spatial and temporal resolution. The source code for Linux and Mac operating systems is released under the BSD license and, along with installation instructions, test images, example configuration files, and a step-by-step tutorial, is freely available at github.com/gmunglani/fret-ibra.…”
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“…CONCLUSIONS: The webserver is available at http://genomics.lshtm.ac.uk/. The source code is available at https://github.com/jodyphelan/covid-profiler. …”
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“…We also make a contribution to bioacoustics generally by offering a comparison of the performance of many state-of-the-art audio representations, including for the first time the LM spectrogram and stockwell representations. All source code for this study is available on GitHub.…”
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“…We used ENCODE ATAC-seq data to benchmark and generate QC recommendations, and developed qATACViewer for the user-friendly interaction with the QC report. The software, source code, and documentation of AIAP are freely available at https://github.com/Zhang-lab/ATAC-seq_QC_analysis.…”
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“…Our results support that RePhine is a useful tool for inferring drug response-related TRs and for potential therapeutic applications. The source code for RePhine is freely available at https://github.com/coexps/RePhine.…”
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“…We finally demonstrate the potential ability of our model to explain functional implications of putative disease-associated genetic variants and discriminate disease-related enhancers. The source code and detailed tutorial of DeepCAPE are freely available at https://github.com/ShengquanChen/DeepCAPE.…”
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“…AVAILABILITY AND IMPLEMENTATION: The R package and source code are available at https://zenodo.org/record/5975977#.YgqR1PXMJjM. …”
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“…STdeconvolve is available as an open-source R software package with the source code available at https://github.com/JEFworks-Lab/STdeconvolve.…”
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“…By benchmarking exhaustive experiments on both simulated and real-life SMS datasets to assess the performance of kngMap with ten other popular SMS mapping tools (e.g., BLASR, BWA-MEM, and minimap2), we demonstrated that kngMap has higher sensitivity that can align more reads and bases to the reference genome; meanwhile, kngMap can produce consecutive alignments for the whole read and span different categories of SVs in the reads. kngMap is implemented in C++ and supports multi-threading; the source code of kngMap can be downloaded for free at: https://github.com/zhang134/kngMap for academic usage.…”
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“…AVAILABILITY AND IMPLEMENTATION: Source code for epigenome-ssm is available at https://github.com/habibdanesh/epigenome-ssm and Zenodo (DOI: 10.5281/zenodo.6507585). …”
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“…This tool is essential to increase the accuracy of categorization of newly identified species and validate updated taxonomies. The source code and data are freely available at https://github.com/ghattab/CAPT.…”
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“…It is open source and an executable jar, source code, quick start, usage tutorial and test data are available (under the GNU General Public License) from https://sourceforge.net/projects/cview/.…”
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“…Additionally, dashboards allow the ability to include downloadable data, interactive tables as well as embedding all source code used in the analysis. The dashboard goes beyond traditional supplemental files and encourages any reader to interact with the results and data providing clarity and transparency of findings. …”
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