tag:joss.theoj.org,2005:/papers/tagged/IndexJournal of Open Source Software2023-07-20T11:29:57ZJournal of Open Source Softwarehttps://joss.theoj.orgtag: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/33412022-12-28T08:58:46Z2022-12-29T00:01:19ZRedOak: a reference-free and alignment-free structure for indexing a collection of similar genomesaccepted0.1.42022-02-15 13:53:48 UTC802022-12-28 08:58:46 UTC720224363ClémentAgretLIRMM, Univ Montpellier, CNRS, Montpellier, France, Cirad, UMR AGAP, Avenue Agropolis, Montpellier, France, CRIStAL, Centre de Recherche en Informatique Signal et Automatique de Lille, Lille, France0000-0002-7404-7253AnnieChateauLIRMM, Univ Montpellier, CNRS, Montpellier, France, Institut de Biologie Computationnelle, Montpellier, France0000-0003-4760-8171GaetanDrocCirad, UMR AGAP, Avenue Agropolis, Montpellier, France0000-0003-1849-1269GautierSarahINRA, UMR AGAP, 2 Place Pierre Viala, Montpellier, France0000-0001-5179-972XManuelRuizCirad, UMR AGAP, Avenue Agropolis, Montpellier, France, Institut de Biologie Computationnelle, Montpellier, France0000-0001-8153-276XAlbanMancheronLIRMM, Univ Montpellier, CNRS, Montpellier, France, Institut de Biologie Computationnelle, Montpellier, France0000-0001-9249-759210.21105/joss.04363https://doi.org/10.6084/m9.figshare.21711767M4, Chttps://joss.theoj.org/papers/10.21105/joss.04363.pdfC/C++, Bioinformatic, k-mers, Genomes, Indextag:joss.theoj.org,2005:Paper/26962022-11-25T08:02:12Z2022-11-26T00:00:47ZClusterValidityIndices.jl: Batch and Incremental Metrics for Unsupervised Learningaccepted0.1.52021-05-28 15:42:10 UTC792022-11-25 08:02:12 UTC720223527SashaPetrenkoMissouri University of Science and Technology0000-0003-2442-8901DonaldC.WunschMissouri University of Science and Technology0000-0002-9726-905110.21105/joss.03527https://doi.org/10.5281/zenodo.7332045Juliahttps://joss.theoj.org/papers/10.21105/joss.03527.pdfCVI, ICVI, Cluster Validity Indices, Cluster Validity Index, Incremental Cluster Validity Indices, Incremental Cluster Validity Index, Machine Learning, Clustering, Metrics, Streaming, Time Seriestag:joss.theoj.org,2005:Paper/33952022-07-25T14:29:52Z2022-07-26T00:01:11ZRIAssigner: A package for gas chromatographic retention index calculationacceptedv0.3.22022-02-24 08:46:27 UTC752022-07-25 14:29:52 UTC720224337HelgeHechtRECETOX, Faculty of Science, Masaryk University, Kotlářská 2, Brno, Czech Republic0000-0001-6744-996XMaksymSkorykRECETOX, Faculty of Science, Masaryk University, Kotlářská 2, Brno, Czech Republic, Institute of Computer Science, Masaryk University, Brno, Czech Republic0000-0003-2056-8018MartinČechRECETOX, Faculty of Science, Masaryk University, Kotlářská 2, Brno, Czech Republic0000-0002-9318-1781ElliottJamesPriceRECETOX, Faculty of Science, Masaryk University, Kotlářská 2, Brno, Czech Republic0000-0001-5691-700010.21105/joss.04337https://doi.org/10.5281/zenodo.6884922Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.04337.pdfgas chromatography, retention index, analytical chemistrytag:joss.theoj.org,2005:Paper/36192022-07-05T15:03:06Z2022-07-06T00:00:54Z`SimilaritySearch.jl`: Autotuned nearest neighbor indexes for Juliaacceptedv0.8.202022-05-23 16:29:38 UTC752022-07-05 15:03:06 UTC720224442EricS.TellezConsejo Nacional de Ciencia y Tecnología, México., INFOTEC Centro de Investigación e Innovación en Tecnologías de la Información y Comunicación, México.0000-0001-5804-9868GuillermoRuizConsejo Nacional de Ciencia y Tecnología, México., CentroGEO Centro de Investigación en Ciencias de Información Geoespacial, México.0000-0001-7422-701110.21105/joss.04442https://doi.org/10.5281/zenodo.6779410Julia, Pythonhttps://joss.theoj.org/papers/10.21105/joss.04442.pdfAutotuned similarity search indexes, K nearest neighbor search, All KNN queries, Near duplicates detection, Closest pair queriestag:joss.theoj.org,2005:Paper/10182019-11-17T18:22:14Z2021-02-15T11:32:08Zhopit: An R Package for Analysis of Reporting Behavior Using Generalized Ordered Probit Modelsaccepted0.9.2.90002019-05-28 16:45:51 UTC432019-11-17 18:22:14 UTC420191508MaciejJ.DańkoMax Planck Institute for Demographic Research, Rostock, Germany0000-0002-7924-902210.21105/joss.01508https://doi.org/10.5281/zenodo.3530634R, C++https://joss.theoj.org/papers/10.21105/joss.01508.pdfself-reported status, reporting heterogeneity, reporting behavior, latent index, latent health, disability weightstag:joss.theoj.org,2005:Paper/5142018-10-04T00:35:10Z2021-02-15T11:33:19ZPython Implementation of Codon Adaptation Indexacceptedv1.0.02018-06-06 18:15:02 UTC302018-10-04 00:35:10 UTC32018905BenjaminD.LeeSchool of Engineering and Applied Sciences, Harvard University0000-0002-7133-839710.21105/joss.00905https://doi.org/10.5281/zenodo.1439494Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.00905.pdfbioinformatics, computational biology, codon adaptation index, molecular biologytag:joss.theoj.org,2005:Paper/5292018-08-06T14:52:24Z2021-02-15T11:33:17ZThe hhi Package: Streamlined Calculation and Visualization of Herfindahl-Hirschman Index Scoresacceptedv1.1.02018-06-28 16:59:00 UTC282018-08-06 14:52:24 UTC32018828PhilipD.WaggonerDepartment of Government, College of William & Mary0000-0002-7825-757310.21105/joss.00828https://doi.org/10.5281/zenodo.1336788Rhttps://joss.theoj.org/papers/10.21105/joss.00828.pdfHerfindahl-Hirschman Index, concentration, economics, political sciencetag:joss.theoj.org,2005:Paper/2662017-10-04T00:00:00Z2021-02-15T11:33:56Zhei: Calculate Healthy Eating Index (HEI) Scoresacceptedv0.1.02017-08-30 01:33:09 UTC182017-10-04 00:00:00 UTC22017417TimFolsomUniversity of Virginia0000-0002-8647-5810VpNagrajUniversity of Virginia0000-0003-0060-566X10.21105/joss.00417https://doi.org/10.6084/m9.figshare.5469208Rhttps://joss.theoj.org/papers/10.21105/joss.00417.pdftag:joss.theoj.org,2005:Paper/2022017-07-13T00:00:00Z2021-02-15T11:34:06ZKindel: indel-aware consensus for nucleotide sequence alignmentsacceptedv0.2.02017-05-26 11:32:21 UTC152017-07-13 00:00:00 UTC22017282BedeConstantinidesEvolution and Genomic Sciences, University of Manchester, Manchester, UK0000-0002-3480-3819DavidL.RobertsonMRC-University of Glasgow Centre for Virus Research, Glasgow, UK0000-0001-6338-022110.21105/joss.00282https://doi.org/10.5281/zenodo.826723Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.00282.pdfbioinformatics, sequence analysis, genome assembly