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3121por Barricelli, Barbara Rita, Casiraghi, Elena, Gliozzo, Jessica, Huber, Veronica, Leone, Biagio Eugenio, Rizzi, Alessandro, Vergani, Barbara“…CONCLUSIONS: The evaluation of the computed results, both through experts’ visual assessments and through the comparison of the computed indexes with those of experts, proved that the prototype is promising, so that experts believe in its potential as a tool to be exploited in the clinical practice as a valid aid for clinicians estimating the ki67-index. The MATLAB source code is open source for research purposes.…”
Publicado 2019
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3122por Zhang, Hang, Wang, Ke, Zhou, Juan, Chen, Jianhua, Xu, Yizhou, Wang, Dong, Li, Xiaoqi, Sun, Renliang, Zhang, Mancang, Wang, Zhuo, Shi, Yongyong“…CONCLUSION: VariFAST can assist researchers efficiently and conveniently to filter the false positive variants, including both germline and somatic ones, in NGS data analysis. The VariFAST source code and the pipeline integrating with GATK Best Practices are available at https://github.com/bioxsjtu/VariFAST.…”
Publicado 2019
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3123“…CONCLUSION: Falco is a significantly updated open source big data processing framework that enables scalable and accelerated alignment and assembly of full-length scRNA-seq data on the cloud. The source code can be found at https://github.com/VCCRI/Falco.…”
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3124“…AVAILABILITY AND IMPLEMENTATION: Source code for our biomedical IE tool is available at https://github.com/BaderLab/saber. …”
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3125por Savojardo, Castrense, Bruciaferri, Niccolò, Tartari, Giacomo, Martelli, Pier Luigi, Casadio, Rita“…A standalone version of DeepMito is available on DockerHub at https://hub.docker.com/r/bolognabiocomp/deepmito. DeepMito source code is available on GitHub at https://github.com/BolognaBiocomp/deepmito SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.…”
Publicado 2020
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3126“…Moreover, SAMPN can generate chemically visible and interpretable results, which can help researchers discover new pharmaceuticals and materials. The source code of the SAMPN prediction pipeline is freely available at Github (https://github.com/tbwxmu/SAMPN).…”
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3127“…AVAILABILITY AND IMPLEMENTATION: Crossmapper is a command line tool implemented in Python 3.6 and available as a conda package, allowing effortless installation. The source code, detailed information and a step-by-step tutorial is available at our GitHub page https://github.com/Gabaldonlab/crossmapper. …”
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3128por Manchanda, Nancy, Portwood, John L., Woodhouse, Margaret R., Seetharam, Arun S., Lawrence-Dill, Carolyn J., Andorf, Carson M., Hufford, Matthew B.“…CONCLUSIONS: The GenomeQC web application is implemented in R/Shiny version 1.5.9 and Python 3.6 and is freely available at https://genomeqc.maizegdb.org/ under the GPL license. All source code and a containerized version of the GenomeQC pipeline is available in the GitHub repository https://github.com/HuffordLab/GenomeQC.…”
Publicado 2020
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3129“…SEQing is customizable in many ways and has also the option to be secured by a password. The source code is available at https://github.com/malewins/SEQing.…”
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3130por Asay, Bryce C., Edwards, Blake Blue, Andrews, Jenna, Ramey, Michelle E., Richard, Jameson D., Podell, Brendan K., Gutiérrez, Juan F. Muñoz, Frank, Chad B., Magunda, Forgivemore, Robertson, Gregory T., Lyons, Michael, Ben-Hur, Asa, Lenaerts, Anne J.“…LIRA was developed to improve the efficiency of histopathology analysis for mouse tuberculosis infection models, this approach has also broader applications to other disease models and tissues. The full source code and documentation is available from https://Github.com/TB-imaging/LIRA.…”
Publicado 2020
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3131“…Our simulation model is capable of addressing additional questions beyond the scope of this article, and we open the simulation software, program manual and source code for free public use.…”
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3132por Queralt-Rosinach, Núria, Stupp, Gregory S, Li, Tong Shu, Mayers, Michael, Hoatlin, Maureen E, Might, Matthew, Good, Benjamin M, Su, Andrew I“…Network data files are at: https://github.com/SuLab/ngly1-graph and source code at: https://github.com/SuLab/bioknowledge-reviewer. …”
Publicado 2020
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3133“…It is implemented using portable Docker containers and can easily be deployed locally or on a cloud infrastructure. The source code for building the service is available under an open-source license on GitHub, with a functional image on Docker Hub and can be used by anyone free of charge.…”
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3134“…We applied our tool on two experimentally validated influenza A virus and hepatitis C virus interactions and we were able to predict potential double mutants for in vitro validation experiments. The source code and documentation of SIM are freely available at github.com/desiro/silentMutations.…”
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3135por Peng, He“…CFSP is implemented in C++ and shell script; the source code and related data are available at https://github.com/HePeng2016/CFSP.…”
Publicado 2020
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3136por Delhomme, Tiffany M, Avogbe, Patrice H, Gabriel, Aurélie A G, Alcala, Nicolas, Leblay, Noemie, Voegele, Catherine, Vallée, Maxime, Chopard, Priscilia, Chabrier, Amélie, Abedi-Ardekani, Behnoush, Gaborieau, Valérie, Holcatova, Ivana, Janout, Vladimir, Foretová, Lenka, Milosavljevic, Sasa, Zaridze, David, Mukeriya, Anush, Brambilla, Elisabeth, Brennan, Paul, Scelo, Ghislaine, Fernandez-Cuesta, Lynnette, Byrnes, Graham, Calvez-Kelm, Florence L, McKay, James D, Foll, Matthieu“…Needlestack, along with its source code is freely available on the GitHub platform: https://github.com/IARCbioinfo/needlestack.…”
Publicado 2020
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3137“…It took 3 h for an experienced researcher for manual analysis. Source code is freely available for download at https://github.com/kablag/AScall. …”
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3138por Amanullah, Md, Yu, Mengqian, Sun, Xiwei, Luo, Aoran, Zhou, Qing, Zhou, Liyuan, Hou, Ling, Wang, Wei, Lu, Weiguo, Liu, Pengyuan, Lu, Yan“…AVAILABILITY AND IMPLEMENTATION: The source code for identifying and quantifying isomiRs and performing miRNA differential expression analysis is available at https://github.com/amanzju/MDEHT. …”
Publicado 2020
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3139por Peabody, Michael A, Lau, Wing Yin Venus, Hoad, Gemma R, Jia, Baofeng, Maguire, Finlay, Gray, Kristen L, Beiko, Robert G, Brinkman, Fiona S L“…AVAILABILITY AND IMPLEMENTATION: Documentation, source code and docker containers are available for running PSORTm locally at https://www.psort.org/psortm/ (freely available, open-source software under GNU General Public License Version 3). …”
Publicado 2020
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3140por Kieser, Silas, Brown, Joseph, Zdobnov, Evgeny M., Trajkovski, Mirko, McCue, Lee Ann“…ATLAS is written in Python and the workflow implemented in Snakemake; it operates in a Linux environment, and is compatible with Python 3.5+ and Anaconda 3+ versions. The source code for ATLAS is freely available, distributed under a BSD-3 license. …”
Publicado 2020
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