“…We also discuss network design considerations, and describe the dependence of accuracy on dataset size and data augmentation. We provide source code, labeled data, and descriptions of our analysis pipeline to facilitate adoption of convolutional neural network analysis for three-dimensional microscopy data.…”
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“…Finally, we identified additional tumor-associated ERVs that correlate with cytolytic activity represented by granzyme and perforin expression in breast cancer tissue samples. The open-source code of ERVmap and the accompanied web tool are made publicly available to quantify proviral ERVs in RNA-sequencing data with ease. …”
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“…AVAILABILITY AND IMPLEMENTATION: To demo Seave with public data, see https://www.seave.bio. Source code is available at http://code.seave.bio and extensive documentation is available at http://documentation.seave.bio. …”
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“…Our program is written in MATLAB, the source code is open source and particularly focuses on providing a streamlined workflow for novice users while also retaining detailed configuration options for advanced users. …”
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“…CONCLUSIONS: ACES has been proven an invaluable tool for analyzing large, pre-filtered DNA methylation data sets and RNA-Sequencing data, due to its ease to link molecular markers to complex phenotypes. The source code is available from https://github.com/GrabherrGroup/ACES.…”
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“…The new module is written in Java, and inherits the cross-platform support from CellMissy. Source code and binaries are freely available under the Apache2 open-source licence at https://github.com/compomics/cellmissy/. …”
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“…Here we present an implementation of this method as a user-friendly, open-source software pipeline for monoallelic gene inference from chromatin (MaGIC). The source code for the MaGIC pipeline and the Shiny app is available at https://github.com/gimelbrantlab/magic. …”
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“…A standalone Docker container as well as the source code of WIlsON are freely available from our Docker hub https://hub.docker. com/r/loosolab/wilson, CRAN https://cran.r-project.org/web/packages/wilson/, and GitHub repository https://github.molgen.mpg.de/loosolab/wilson-apps, respectively.…”
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“…AVAILABILITY AND IMPLEMENTATION: Source code and datasets are freely available upon paper acceptance at the URL: https://github.com/Gege7177/Dot2dot. …”
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“…AVAILABILITY AND IMPLEMENTATION: The source code and user manual: https://github.com/jianlin-cheng/GenomeFlow. …”
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“…Our developed model can be applied to other sleep EEG signals and aid the sleep specialists to arrive at an accurate diagnosis. The source code is available at https://github.com/SajadMo/SleepEEGNet.…”
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“…AVAILABILITY AND IMPLEMENTATION: VCPA is released under the MIT license and is available for academic and nonprofit use for free. The pipeline source code and step-by-step instructions are available from the National Institute on Aging Genetics of Alzheimer’s Disease Data Storage Site (http://www.niagads.org/VCPA). …”
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“…AVAILABILITY AND IMPLEMENTATION: GBS-SNP-CROP source code and user manual are available at https://github.com/halelab/GBS-SNP-CROP. …”
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“…This improved version called CFM-ID 3.0 is freely available as a web server. Its source code is also accessible online.…”
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“…It has also been applied in post-experimental data analysis. The source code is available via https://github.com/LiuLab-CSRC/ClickX under a GNU General Public License.…”
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“…Because our source data are well-structured and well-defined, the only parameter needed in the query is a single identifier for the grant itself. The open source code for producing this document is at http://dx.doi.org/10.5281/zenodo.2593545. …”
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“…Aneuvis is freely available as a web application at https://dpique.shinyapps.io/aneuvis/ and the source code for the application is available at https://github.com/dpique/aneuvis. …”
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“…By providing a format that allows for easy sharing of code and associated data, we intend to promote open and reproducible research. The source code and documentation can be found via the project’s GitHub page.…”
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“…AVAILABILITY AND IMPLEMENTATION: Block HSIC Lasso is implemented in the Python 2/3 package pyHSICLasso, available on PyPI. Source code is available on GitHub (https://github.com/riken-aip/pyHSICLasso). …”
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“…We have thoroughly tested our GlycanFormatConverter and were able to show that it was possible to convert all the glycans registered in the GlyTouCan repository, with exceptions owing only to the limitations of the original format. The source code for this conversion tool has been released as an open source tool. …”
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