tag:joss.theoj.org,2005:/papers/tagged/bioinformaticsJournal of Open Source Software2024-01-24T17:19:02ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/49472024-01-24T17:19:02Z2024-02-25T07:02:22ZViash: A meta-framework for building reusable workflow modulesaccepted0.8.12023-11-21 12:26:06 UTC932024-01-24 17:19:02 UTC920246089RobrechtCannoodtData Intuitive, Lebbeke, Belgium, Data Mining and Modelling for Biomedicine group, VIB Center for Inflammation Research, Ghent, Belgium, Department of Applied Mathematics, Computer Science, and Statistics, Ghent University, Ghent, Belgium0000-0003-3641-729XHendrikCannoodtData Intuitive, Lebbeke, Belgium0000-0002-0032-6719DriesSchaumontData Intuitive, Lebbeke, Belgium0000-0002-4389-0440KaiWaldrantData Intuitive, Lebbeke, Belgium0009-0003-8555-1361EricVan de KerckhoveData Intuitive, Lebbeke, BelgiumAndyBoschmansData Intuitive, Lebbeke, Belgium0009-0008-8793-4661DriesDe MaeyerDiscovery Technology and Molecular Pharmacology, Janssen Research & Development, Pharmaceutical Companies of Johnson & Johnson, Beerse, Belgium0000-0002-1314-3348ToniVerbeirenData Intuitive, Lebbeke, Belgium0000-0002-7007-686610.21105/joss.06089https://doi.org/10.5281/zenodo.10563479Scala, Nextflowhttps://joss.theoj.org/papers/10.21105/joss.06089.pdfBioinformatics, Workflows, Software development, Reproducibility, Cloud computing, Dockertag:joss.theoj.org,2005:Paper/48382024-01-22T15:00:12Z2024-01-23T11:55:19Zcstag and cstag-cli: tools for manipulating and visualizing cs tagsacceptedv1.0.42023-10-06 03:25:34 UTC932024-01-22 15:00:12 UTC920246066AkihiroKunoDepartment of Anatomy and Embryology, University of Tsukuba, Tsukuba, Ibaraki, Japan, Laboratory Animal Resource Center, Trans-border Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan.0000-0002-4674-688210.21105/joss.06066https://doi.org/10.5281/zenodo.10544838Pythonhttps://joss.theoj.org/papers/10.21105/joss.06066.pdfpython, genomics, sequencing, bioinformaticstag:joss.theoj.org,2005:Paper/45402024-01-12T22:11:20Z2024-01-15T11:54:18Zcellanneal: A user-friendly deconvolution software for transcriptomics dataacceptedv1.0.02023-06-12 17:35:47 UTC932024-01-12 22:11:20 UTC920245610LisaBuchauerDepartment of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel, Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany0000-0002-4722-8390ShalevItzkovitzDepartment of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel0000-0003-0685-252210.21105/joss.05610https://doi.org/10.5281/zenodo.10405043Pythonhttps://joss.theoj.org/papers/10.21105/joss.05610.pdfbioinformatics, computational biology, mixture deconvolution, bulk deconvolution, transcriptomics, RNA sequencing, omics methodstag:joss.theoj.org,2005:Paper/48632023-12-19T12:19:57Z2024-01-11T16:55:09ZMiscMetabar: an R package to facilitate visualization and reproducibility in metabarcoding analysisacceptedv0.52023-10-23 15:45:54 UTC922023-12-19 12:19:57 UTC820236038AdrienTaudièreIdEst, Saint-Bonnet-de-Salendrinque, 30460 France0000-0003-1088-118210.21105/joss.06038https://doi.org/10.5281/zenodo.10370781Rhttps://joss.theoj.org/papers/10.21105/joss.06038.pdfBioinformatic, Metagenomics, Barcoding, Reproducibilitytag:joss.theoj.org,2005:Paper/43102023-10-24T14:44:56Z2024-02-07T13:20:12Zgesel: a JavaScript package for client-side gene set enrichmentaccepted0.2.32023-03-15 18:20:39 UTC902023-10-24 14:44:56 UTC820235777AaronTin LongLunGenentech Inc., South San Francisco, United States of America0000-0002-3564-4813JayaramKancherlaGenentech Inc., South San Francisco, United States of America0000-0001-5855-503110.21105/joss.05777https://doi.org/10.5281/zenodo.10032294JavaScripthttps://joss.theoj.org/papers/10.21105/joss.05777.pdfbioinformaticstag:joss.theoj.org,2005:Paper/43162023-09-11T12:58:31Z2023-09-12T00:01:38ZFrESCO: Framework for Exploring Scalable Computational Oncologyacceptedv1.0.02023-03-16 17:23:44 UTC892023-09-11 12:58:31 UTC820235345AdamSpannausOak Ridge National Laboratory, Oak Ridge, TN, United States of America0000-0002-2521-3657JohnGounleyOak Ridge National Laboratory, Oak Ridge, TN, United States of AmericaMayankaChandraShekarOak Ridge National Laboratory, Oak Ridge, TN, United States of AmericaZacharyR.FoxOak Ridge National Laboratory, Oak Ridge, TN, United States of AmericaJamaludinMohd-YusofLos Alamos National Laboratory, Los Alamos, NM, United States of AmericaNoahSchaefferkoetterOak Ridge National Laboratory, Oak Ridge, TN, United States of AmericaHeidiA.HansonOak Ridge National Laboratory, Oak Ridge, TN, United States of America10.21105/joss.05345https://doi.org/10.5281/zenodo.8325993Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.05345.pdfbioinformatics, natural language processing, deep learning, computational oncologytag:joss.theoj.org,2005:Paper/44852023-09-05T09:36:31Z2024-02-22T09:48:52ZPowering single-cell analyses in the browser with WebAssemblyaccepted3.0.132023-05-15 20:27:07 UTC892023-09-05 09:36:31 UTC820235603AaronTin LongLunGenentech Inc., South San Francisco, United States of America0000-0002-3564-4813JayaramKancherlaGenentech Inc., South San Francisco, United States of America0000-0001-5855-503110.21105/joss.05603https://doi.org/10.5281/zenodo.8273645JavaScripthttps://joss.theoj.org/papers/10.21105/joss.05603.pdfWebAssembly, bioinformatics, single-celltag:joss.theoj.org,2005:Paper/41882023-07-20T11:29:57Z2023-07-27T07:02:54ZSeqPanther: Sequence manipulation and mutation statistics toolsetacceptedv1.0.02023-02-03 07:59:06 UTC872023-07-20 11:29:57 UTC820235305JamesEmmanuelSanKwaZulu Natal Research and Innovation Sequencing Platform, KRISP, University of KwaZulu Natal, Durban, South Africa, Centre for Epidemic Response and Innovation, CERI, University of Stellenbosch, Stellenbosch, South Africa0000-0002-5736-664XStephanievan WykCentre for Epidemic Response and Innovation, CERI, University of Stellenbosch, Stellenbosch, South Africa0000-0002-2655-8518HouriiyahTegallyKwaZulu Natal Research and Innovation Sequencing Platform, KRISP, University of KwaZulu Natal, Durban, South Africa, Centre for Epidemic Response and Innovation, CERI, University of Stellenbosch, Stellenbosch, South Africa0000-0002-7102-8540SimeonEcheYale University School of Medicine, New Haven, Connecticut, United States of America0000-0001-5494-8372EduanWilkinsonKwaZulu Natal Research and Innovation Sequencing Platform, KRISP, University of KwaZulu Natal, Durban, South Africa, Centre for Epidemic Response and Innovation, CERI, University of Stellenbosch, Stellenbosch, South Africa0000-0002-2503-9441AquillahM.KanziKwaZulu Natal Research and Innovation Sequencing Platform, KRISP, University of KwaZulu Natal, Durban, South Africa0000-0001-6081-9438Tuliode OliveiraKwaZulu Natal Research and Innovation Sequencing Platform, KRISP, University of KwaZulu Natal, Durban, South Africa, Centre for Epidemic Response and Innovation, CERI, University of Stellenbosch, Stellenbosch, South Africa, Department of Global Health, University of Washington, Seattle, WA, United States of America0000-0002-3027-5254AnmolM.KiranSchool of Biochemistry and Cell Biology, University College Cork, Cork, T12 XF62, Ireland0000-0003-2680-230310.21105/joss.05305https://doi.org/10.5281/zenodo.8126922Pythonhttps://joss.theoj.org/papers/10.21105/joss.05305.pdfBioinformatics, sequence analysis, NGS, codon, amino acid substitution, nucleotide substitution, INDELtag:joss.theoj.org,2005:Paper/45792023-07-11T15:34:01Z2023-07-14T13:35:51ZTAXPASTA: TAXonomic Profile Aggregation and STAndardisationaccepted0.4.02023-07-05 17:39:09 UTC872023-07-11 15:34:01 UTC820235627MoritzE.BeberUnseen Bio ApS, Copenhagen, Denmark0000-0003-2406-1978MaximeBorryMicrobiome Sciences Group, Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Jena, Germany0000-0001-9140-7559SofiaStamouliDepartment of Microbiology, Tumor and Cell Biology, Karolinska Institute, Solna, Sweden0009-0006-0893-3771JamesA. FellowsYatesMicrobiome Sciences Group, Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Jena, Germany, Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, Jena, Germany0000-0001-5585-627710.21105/joss.05627https://doi.org/10.5281/zenodo.8105840https://joss.theoj.org/papers/10.21105/joss.05627.pdfbioinformatics, metagenomics, profiling, classification, standardisation, taxonomy, Pythontag:joss.theoj.org,2005:Paper/41792023-05-10T21:48:40Z2023-05-11T09:01:03Zmutyper: assigning and summarizing mutation types for analyzing germline mutation spectraacceptedv0.7.02023-01-24 22:40:00 UTC852023-05-10 21:48:40 UTC820235227WilliamS.DeWittDepartment of Electrical Engineering & Computer Sciences, University of California, Berkeley, CA, United States of America0000-0002-6802-9139LukeZhuDepartment of Bioengineering, University of Washington, Seattle, WA, United States of America0000-0002-6324-1464MitchellR.VollgerDepartment of Genome Sciences, University of Washington, Seattle, WA, United States of America0000-0002-8651-1615MichaelE.GoldbergDepartment of Genome Sciences, University of Washington, Seattle, WA, United States of America, Departments of Human Genetics and of Biomedical Informatics, University of Utah, Salt Lake City, UT, United States of America0000-0003-3310-6349AndreaTalentiThe Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom0000-0003-1309-3667AnnabelC.BeichmanDepartment of Genome Sciences, University of Washington, Seattle, WA, United States of America0000-0002-6991-587XKelleyHarrisDepartment of Genome Sciences, University of Washington, Seattle, WA, United States of America0000-0003-0302-252310.21105/joss.05227https://doi.org/10.5281/zenodo.7921769Pythonhttps://joss.theoj.org/papers/10.21105/joss.05227.pdfgenomics, computational biology, bioinformatics, mutation spectrum, python