tag:joss.theoj.org,2005:/papers/tagged/taxonomyJournal of Open Source Software2024-01-12T08:36:31ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/50002024-01-12T08:36:31Z2024-01-13T00:00:51Zdwctaxon, an R package for editing and validating taxonomic data in Darwin Core formatacceptedv2.0.32023-12-15 08:13:29 UTC932024-01-12 08:36:31 UTC920246215JoelH.NittaGraduate School of Global and Transdisciplinary Studies, Chiba University, Japan0000-0003-4719-7472WataruIwasakiDepartment of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan, Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan, Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan0000-0002-9169-924510.21105/joss.06215https://doi.org/10.5281/zenodo.6388271Rhttps://joss.theoj.org/papers/10.21105/joss.06215.pdftaxonomy, biodiversitytag: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/38582023-02-20T17:45:21Z2023-04-18T07:24:31ZMetaGenePipe: An Automated, Portable Pipeline for Contig-based Functional and Taxonomic Analysisacceptedv.1.0.02022-09-08 01:21:00 UTC822023-02-20 17:45:21 UTC820234851BabakShabanMelbourne Data Analytics Platform, The University of Melbourne0000-0002-7393-810XMaria del MarQuirogaMelbourne Data Analytics Platform, The University of Melbourne0000-0002-8943-2808RobertTurnbullMelbourne Data Analytics Platform, The University of Melbourne0000-0003-1274-6750EdoardoTescariMelbourne Data Analytics Platform, The University of Melbourne0000-0003-1157-4897Kim-AnhLêCaoSchool of Mathematics and Statistics, Melbourne Integrative Genomics, The University of Melbourne0000-0003-3923-1116HeroenVerbruggenSchool of BioSciences, The University of Melbourne0000-0002-6305-474910.21105/joss.04851https://doi.org/10.26188/22032425wdl, Jupyter Notebook, Pythonhttps://joss.theoj.org/papers/10.21105/joss.04851.pdfmetagenomics, WDL, Singularity, Containerizationtag:joss.theoj.org,2005:Paper/37112022-11-13T15:46:15Z2022-11-14T22:01:12ZFastsubtrees: simple and efficient subtrees extractions in Python with applications to NCBI taxonomyaccepted1.02022-07-08 15:18:39 UTC792022-11-13 15:46:15 UTC720224755AmanModiDepartment of Bioinformatics (IMG), University of Göttingen, Göttingen, Germany0000-0002-9843-7133GiorgioGonnellaDepartment of Bioinformatics (IMG), University of Göttingen, Göttingen, Germany, Center for Bioinformatics (ZBH), University of Hamburg, Hamburg, Germany0000-0003-3900-539710.21105/joss.04755https://doi.org/10.5281/zenodo.7312100Pythonhttps://joss.theoj.org/papers/10.21105/joss.04755.pdftree, subtrees extraction, bioinformatics, taxonomytag:joss.theoj.org,2005:Paper/35112022-06-01T20:05:57Z2022-06-02T00:01:04Zsam2lca: Lowest Common Ancestor for SAM/BAM/CRAM alignment filesacceptedv1.0.0b2022-04-21 15:14:38 UTC742022-06-01 20:05:57 UTC720224360MaximeBorryMicrobiome Sciences Group, Max Planck Institute for Evolutionary Anthropology, Department of Archaeogenetics, Leipzig, Germany0000-0001-9140-7559AlexanderHübnerMicrobiome Sciences Group, Max Planck Institute for Evolutionary Anthropology, Department of Archaeogenetics, Leipzig, Germany, Faculty of Biological Sciences, Friedrich-Schiller Universität Jena, Jena, Germany0000-0003-3572-9996ChristinaWarinnerMicrobiome Sciences Group, Max Planck Institute for Evolutionary Anthropology, Department of Archaeogenetics, Leipzig, Germany, Faculty of Biological Sciences, Friedrich-Schiller Universität Jena, Jena, Germany, Department of Anthropology, Harvard University, Cambridge, MA, United States of America0000-0002-4528-587710.21105/joss.04360https://doi.org/10.5281/zenodo.6585307Pythonhttps://joss.theoj.org/papers/10.21105/joss.04360.pdfmetagenomics, microbiome, alignment, sam, bam, cram, htslib, taxonomy, LCA, ancestortag:joss.theoj.org,2005:Paper/31102021-12-24T16:41:35Z2021-12-25T00:01:13ZSepia, a taxonomy oriented read classifier in Rustacceptedv0.0.22021-10-14 16:38:44 UTC682021-12-24 16:41:35 UTC620213839HenkC. denBakkerCenter for Food Safety, University of Georgia, Griffin, GA, USA0000-0002-4086-1580LeeS.KatzCenter for Food Safety, University of Georgia, Griffin, GA, USA, Enteric Diseases Laboratory Branch (EDLB), Centers for Disease Control and Prevention, Atlanta, GA, USA0000-0002-2533-916110.21105/joss.03839https://doi.org/10.5281/zenodo.5787248Python, Rusthttps://joss.theoj.org/papers/10.21105/joss.03839.pdfread classification, taxonomytag:joss.theoj.org,2005:Paper/21392021-01-08T09:10:54Z2021-02-15T11:29:47ZEUKulele: Taxonomic annotation of the unsung eukaryotic microbesacceptedv1.0.02020-10-29 10:55:19 UTC572021-01-08 09:10:54 UTC620212817AriannaI.KrinosBiology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA, MIT-WHOI Joint Program in Oceanography, Cambridge and Woods Hole, MA, USA0000-0001-9767-8392SarahK.HuMarine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA, Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA, USA0000-0002-4439-1360NatalieR.CohenMarine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA0000-0001-6156-9186HarrietAlexanderBiology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA0000-0003-1308-800810.21105/joss.02817https://doi.org/10.5281/zenodo.4422091Pythonhttps://joss.theoj.org/papers/10.21105/joss.02817.pdfTaxonomy, Metagenomics, Metatranscriptomicstag:joss.theoj.org,2005:Paper/9052019-03-31T18:16:09Z2021-02-15T11:32:29ZMicrobiomeR: An R Package for Simplified and Standardized Microbiome Analysis Workflowsaccepted0.5.12019-02-27 22:43:22 UTC352019-03-31 18:16:09 UTC420191299RobertA.GilmoreDepartment of Neurobiology, University of Mississippi Medical Center, Jackson, MS 39216, USA0000-0001-8096-0180ShauritaHutchinsDepartment of Neurobiology, University of Mississippi Medical Center, Jackson, MS 39216, USA0000-0002-7687-0059XiaoZhangDepartment of Neurobiology, University of Mississippi Medical Center, Jackson, MS 39216, USA0000-0001-5710-6496EricVallenderDepartment of Neurobiology, University of Mississippi Medical Center, Jackson, MS 39216, USA0000-0003-3506-054010.21105/joss.01299https://doi.org/10.5281/zenodo.2600432Rhttps://joss.theoj.org/papers/10.21105/joss.01299.pdfbioinformatics, microbiome, taxonomytag:joss.theoj.org,2005:Paper/7292018-11-20T15:13:22Z2021-02-15T11:32:47Zrcites: An R package to access the CITES Speciesplus databaseaccepted1.0.02018-11-19 23:38:02 UTC312018-11-20 15:13:22 UTC320181091JonasGeschkeMuseum für Naturkunde Berlin - Leibniz Institute for Research on Evolution and Biodiversity, Berlin, Germany0000-0002-5654-9313KevinCazellesDepartment of Integrative Biology, University Of Guelph, Guelph, Ontario, Canada0000-0001-6619-9874IgnasiBartomeusEstación Biológica de Doñana (EBD-CSIC), Sevilla, Spain0000-0001-7893-438910.21105/joss.01091https://doi.org/10.5281/zenodo.1490219Rhttps://joss.theoj.org/papers/10.21105/joss.01091.pdfCITES Speciesplus, taxonomy, endangered species, illegal wildlife trade, species legislation, species distributiontag:joss.theoj.org,2005:Paper/6182018-11-13T19:50:24Z2021-02-15T11:33:01ZhillR: taxonomic, functional, and phylogenetic diversity and similarity through Hill Numbersacceptedv0.3.02018-09-12 15:36:43 UTC312018-11-13 19:50:24 UTC320181041DaijiangLiDepartment of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 326110000-0002-0925-342110.21105/joss.01041https://doi.org/10.5281/zenodo.1486200Rhttps://joss.theoj.org/papers/10.21105/joss.01041.pdfHill numbers, biodiversity, phylogenetic diversity, functional diversity