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3741por Holm, Johanna B., France, Michael T., Gajer, Pawel, Ma, Bing, Brotman, Rebecca M., Shardell, Michelle, Forney, Larry, Ravel, Jacques“…Finally, we report a mgSs and mgCST classifier for which source code is provided and may be adapted for use by the microbiome research community. …”
Publicado 2023
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3742por Tang, Chen, Fu, Shaliu, Jin, Xuan, Li, Wannian, Xing, Feiyang, Duan, Bin, Cheng, Xiaojie, Chen, Xiaohan, Wang, Shuguang, Zhu, Chenyu, Li, Gaoyang, Chuai, Guohui, He, Yayi, Wang, Ping, Liu, Qi“…A user-friendly web server of comboSC for both clinical and research users is available at www.combosc.top. The source code is also available on GitHub at https://github.com/bm2-lab/comboSC. …”
Publicado 2023
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3743“…For 171 sequences, this distance is larger than two, and for only 11 sequences, this distance is larger than five. Availability: The source code is available on http://compbio.cs.wayne.edu/software/rna-newton-polytope. …”
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3744“…In particular, distinct contributions of different meta-path instances and meta-path types were combined with attention mechanisms. The data sets and source code that support the findings of this study are available at https://github.com/dangdangzhang/M2GMDA. …”
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3745por Lane, Jennifer C E, Weaver, James, Kostka, Kristin, Duarte-Salles, Talita, Abrahao, Maria Tereza F, Alghoul, Heba, Alser, Osaid, Alshammari, Thamir M, Areia, Carlos, Biedermann, Patricia, Banda, Juan M, Burn, Edward, Casajust, Paula, Fister, Kristina, Hardin, Jill, Hester, Laura, Hripcsak, George, Kaas-Hansen, Benjamin Skov, Khosla, Sajan, Kolovos, Spyros, Lynch, Kristine E, Makadia, Rupa, Mehta, Paras P, Morales, Daniel R, Morgan-Stewart, Henry, Mosseveld, Mees, Newby, Danielle, Nyberg, Fredrik, Ostropolets, Anna, Woong Park, Rae, Prats-Uribe, Albert, Rao, Gowtham A, Reich, Christian, Rijnbeek, Peter, Sena, Anthony G, Shoaibi, Azza, Spotnitz, Matthew, Subbian, Vignesh, Suchard, Marc A, Vizcaya, David, Wen, Haini, de Wilde, Marcel, Xie, Junqing, You, Seng Chan, Zhang, Lin, Lovestone, Simon, Ryan, Patrick, Prieto-Alhambra, Daniel“…The full study protocol and analysis source code can be found at https://github.com/ohdsi-studies/Covid19EstimationHydroxychloroquine2.…”
Publicado 2020
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3746“…Overall, this study implemented a quick, effective, and economical approach for analyzing population-level disparities during a public health event. The source code developed in this study was released for free public use at GitHub. …”
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3747por Chrisman, Brianna S., Paskov, Kelley M., Stockham, Nate, Jung, Jae-Yoon, Varma, Maya, Washington, Peter Y., Tataru, Christine, Iwai, Shoko, DeSantis, Todd Z., David, Maude, Wall, Dennis P.“…CONCLUSIONS: SBBs provide a powerful method for aggregating microbes to perform differential abundance analysis as well as phenotype prediction. Our source code can be freely downloaded from http://github.com/briannachrisman/16s_biomarkers.…”
Publicado 2021
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3748“…CONCLUSIONS: ViSCAR empowers researchers to capture and characterize the stochasticity, uncover the mechanisms leading to cellular phenotypes of interest, and decipher a large heterogeneous microbial communities' dynamic behavior. ViSCAR source code is available from GitLab at https://gitlab.com/ManolakosLab/viscar. …”
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3749“…It attempts to answer the questions related to applications of GANs, popular GAN architectures, frequently used image modalities, and the availability of source code. METHODS: A search was conducted on 5 databases, namely PubMed, IEEEXplore, Association for Computing Machinery (ACM) Digital Library, Scopus, and Google Scholar. …”
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3750“…The proposed methodology can be used in the other applications in the BLAST+ suite or any other application as long as source code is available.…”
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3751por Inglese, V“…To assess the fulfillment of these project goals on the release 3.0 of FFMM, the internal quality of its source code was evaluated by means of suitable metrics according to the reference model defined in the standard ISO 9126. …”
Publicado 2009
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3752“…Tables for all quantities versus centrality at present and foreseen collision energies involving Pb nuclei, as well as for collisions of XeXe at sNN=5.44TeV, and AuAu and CuCu at sNN=0.2TeV, are provided. The source code for the improved Monte Carlo Glauber model is made publicly available.…”
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3753por Neves, Mariana, Klippert, Antonina, Knöspel, Fanny, Rudeck, Juliane, Stolz, Ailine, Ban, Zsofia, Becker, Markus, Diederich, Kai, Grune, Barbara, Kahnau, Pia, Ohnesorge, Nils, Pucher, Johannes, Schönfelder, Gilbert, Bert, Bettina, Butzke, Daniel“…The corpus is available for download (https://doi.org/10.5281/zenodo.7152295), as well as the source code (https://github.com/mariananeves/goldhamster) and the model (https://huggingface.co/SMAFIRA/goldhamster). …”
Publicado 2023
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3754por Castelli, Pierluigi, De Ruvo, Andrea, Bucciacchio, Andrea, D’Alterio, Nicola, Cammà, Cesare, Di Pasquale, Adriano, Radomski, Nicolas“…CONCLUSIONS: In addition to recommendations about machine learning practices for L. monocytogenes source attribution based on genomic data, the present study also provides a freely available workflow to solve other balanced or unbalanced multiclass phenotypes from binary and categorical genomic profiles of other microorganisms without source code modifications. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-023-09667-w.…”
Publicado 2023
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3755por Zhou, Ji, Applegate, Christopher, Alonso, Albor Dobon, Reynolds, Daniel, Orford, Simon, Mackiewicz, Michal, Griffiths, Simon, Penfield, Steven, Pullen, Nick“…To serve the plant research community, our modulated source code, detailed comments, executables (.exe for Windows; .app for Mac), and experimental results are freely available at https://github.com/Crop-Phenomics-Group/Leaf-GP/releases. …”
Publicado 2017
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3756“…Finally, we combine meta-path based node embedding and pair embedding with the cost function to learn and predict miRNA-disease association. The source code and data sets that verify the results of our research are shown at https://github.com/liubailong/CEMDA. …”
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3757por Hajarolasvadi, Noushin, Sunkara, Vikram, Khavnekar, Sagar, Beck, Florian, Brandt, Robert, Baum, Daniel“…To present a reproducible work, source code, trained models, data as well as visualization results are made publicly available. …”
Publicado 2022
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3758por Fahmi, Naima Ahmed, Ahmed, Khandakar Tanvir, Chang, Jae-Woong, Nassereddeen, Heba, Fan, Deliang, Yong, Jeongsik, Zhang, Wei“…APA-Scan is implemented in Python3. Source code and a comprehensive user’s manual are freely available at https://github.com/compbiolabucf/APA-Scan. …”
Publicado 2022
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3759por Britto-Borges, Thiago, Ludt, Annekathrin, Boileau, Etienne, Gjerga, Enio, Marini, Federico, Dieterich, Christoph“…CONCLUSION: Magnetique (https://shiny.dieterichlab.org/app/magnetique) is the first online application to provide an interactive view of the HF transcriptome at the RNA isoform level and to include transcription factor signaling and RBP:RNA interaction networks. The source code for both the analyses (https://github.com/dieterich-lab/magnetiqueCode2022) and the web application (https://github.com/AnnekathrinSilvia/magnetique) is available to the public. …”
Publicado 2022
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3760por Ayala-Ortiz, Christian, Graf-Grachet, Nathalia, Freire-Zapata, Viviana, Fudyma, Jane, Hildebrand, Gina, AminiTabrizi, Roya, Howard-Varona, Cristina, Corilo, Yuri E., Hess, Nancy, Duhaime, Melissa B., Sullivan, Matthew B., Tfaily, Malak M.“…It will further advance our knowledge of how microbial communities influence and are influenced by the chemical makeup of the surrounding system. The source code and User’s guide of MetaboDirect are freely available through (https://github.com/Coayala/MetaboDirect) and (https://metabodirect.readthedocs.io/en/latest/), respectively. …”
Publicado 2023
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