“…We tested SiNPle on several simulated and real-life viral datasets to show that it is faster and more sensitive than existing methods. The source code for SiNPle is freely available to download and compile, or as a Conda/Bioconda package.…”
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“…AVAILABILITY AND IMPLEMENTATION: Source code is available at https://github.com/zsethna/OLGA. …”
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“…AVAILABILITY AND IMPLEMENTATION: Source code is available at Bioinformatics online. USDL algorithm has been also integrated in SCENERY (http://scenery.csd.uoc.gr/); an online tool for single-cell mass cytometry analytics. …”
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“…TargetMine with its auxiliary toolkit is available at https://targetmine.mizuguchilab.org. The TargetMine source code is available at https://github.com/chenyian-nibio/targetmine-gradle.…”
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“…Here, we document the Transitivity code, written in Python, a free open-source code compatible with Windows, Linux and macOS platforms. …”
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“…The software is freely available at http://mizuguchilab.org/tools/cline/. Also, the source code, documentation and installation instructions are available on GitHub at https://github.com/RodolfoAllendes/cline/.…”
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“…AVAILABILITY AND IMPLEMENTATION: OncodriveCLUSTL is available as an installable Python 3.5 package. The source code and running examples are freely available at https://bitbucket.org/bbglab/oncodriveclustl under GNU Affero General Public License. …”
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“…Finally, we report the first real, non-simulated network test results for the most attractive SA protocol, our implementations of which are available as open-source code for two platforms: Arduino and TinyOS. This work demonstrates the practical usability (and the attractive performance) of SA, serving as a ripe technology enabler for (among others) networks with many potentially compromised low-level devices.…”
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“…When applied to two real datasets, RRIntCC was able to find several significant regions, while BOOST failed to identify any significant results. The source code and the sample data of RRIntCC are available at http://bioinformatics.ust.hk/RRIntCC.html. …”
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“…Finally, for the benefit of the research community, we make publicly available the source code of the proposed automatic 3DMM construction pipeline, as well as the constructed global 3DMM and a variety of bespoke models tailored by age, gender and ethnicity.…”
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“…DISPOT is implemented in two modes, basic and auto-extraction. The source code for both modes is available on GitHub: https://github.com/korkinlab/dispot and standalone docker images on DockerHub: https://hub.docker.com/r/korkinlab/dispot. …”
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“…TCRWMDA was applied to the analysis of four types of cancer, the results proved that TCRWMDA is an effective tool to predict the potential miRNA-disease association. The source code and dataset of TCRWMDA are available at: https://github.com/ylm0505/TCRWMDA.…”
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“…MAGO is an open-source-software package released in three different ways, as a singularity image and a Docker container for HPC purposes as well as for running MAGO on a commodity hardware, and a virtual machine for gaining a full access to MAGO underlying structure and source code. MAGO is open to suggestions for extensions and is amenable for use in both research and teaching of genomics and molecular evolution of genomes assembled from small single-cell projects or large-scale and complex environmental metagenomes.…”
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“…Cross-checking against the proposed method would have caught the numerical errors in both cases. The source code of the algorithm is available on GitHub, together with self-contained command-line executables. …”
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“…The Iroki web application and documentation are available at https://www.iroki.net or through the VIROME portal http://virome.dbi.udel.edu. Iroki’s source code is released under the MIT license and is available at https://github.com/mooreryan/iroki.…”
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“…The present study suggests that DeepCPI is a useful and powerful tool for drug discovery and repositioning. The source code of DeepCPI can be downloaded from https://github.com/FangpingWan/DeepCPI.…”
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“…The experimental result shows that our pipeline outperforms the existing subclonal reconstruction programs both on simulated data and TCGA data. Source code is publicly available as a Python package at https://github.com/dustincys/msphy-SCNAClonal.…”
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“…CONCLUSIONS: BLAMM is an efficient tool for identifying PWM matches in large DNA sequences. Its C++ source code is available under the GNU General Public License Version 3 at https://github.com/biointec/blamm.…”
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“…AVAILABILITY AND IMPLEMENTATION: QMEANDisCo is available as web-server at https://swissmodel.expasy.org/qmean. The source code can be downloaded from https://git.scicore.unibas.ch/schwede/QMEAN. …”
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