tag:joss.theoj.org,2005:/papers/edited_by/@lpantanoJournal of Open Source Software2023-10-23T10:25:02ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/42822023-10-23T10:25:02Z2023-10-24T00:01:06ZQuaC: A Pipeline Implementing Quality Control Best Practices for Genome Sequencing and Exome Sequencing Dataaccepted1.32023-03-06 22:06:16 UTC902023-10-23 10:25:02 UTC820235313ManavalanGajapathyCenter for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America, Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America0000-0002-8606-0113BrandonM.WilkCenter for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America, Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America0000-0002-4110-2324ElizabethA.WortheyCenter for Computational Genomics and Data Science, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America, Department of Genetics, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, United States of America0000-0003-4083-776410.21105/joss.05313https://doi.org/10.5281/zenodo.10002036Jinja, Pythonhttps://joss.theoj.org/papers/10.21105/joss.05313.pdfsnakemake, quality control, genome sequencing, exome sequencing, QC review, multiqc, singularity, bam, vcftag:joss.theoj.org,2005:Paper/44392023-10-05T09:52:45Z2023-10-06T00:01:05ZNORDic: a Network-Oriented package for the Repurposing of Drugsacceptedv2.4.22023-04-18 11:32:05 UTC902023-10-05 09:52:45 UTC820235532ClémenceRédaUniversité Paris Cité, Neurodiderot, Inserm, F-75019 Paris, France0000-0003-3238-0258AndréeDelahaye-DuriezUniversité Paris Cité, Neurodiderot, Inserm, F-75019 Paris, France, Université Sorbonne Paris Nord, UFR de santé, médecine et biologie humaine, F-93000 Bobigny, France, Unité fonctionnelle de médecine génomique et génétique clinique, Hôpital Jean Verdier, AP-HP, F-93140 Bondy, France0000-0003-4324-737210.21105/joss.05532https://doi.org/10.5281/zenodo.8355529Jupyter Notebook, Pythonhttps://joss.theoj.org/papers/10.21105/joss.05532.pdfnetwork analysis, boolean network, network inference, biomarker identification, drug repurposingtag: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, pythontag:joss.theoj.org,2005:Paper/39452022-12-28T09:07:11Z2022-12-29T00:01:16ZMetagenomic classification with KrakenUniq on low-memory computersacceptedv1.0.12022-10-06 17:50:41 UTC802022-12-28 09:07:11 UTC720224908ChristopherPockrandtCenter for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA, Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USAAlekseyV.ZiminCenter for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA, Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USAStevenL.SalzbergCenter for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA, Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA, Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA, Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21218, USA10.21105/joss.04908https://doi.org/10.5281/zenodo.7459217Perlhttps://joss.theoj.org/papers/10.21105/joss.04908.pdfmetagenomics, classification, speciestag: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/32752022-10-08T07:54:59Z2022-10-10T12:31:52ZVPsearch: fast exact sequence similarity search for genomic sequencesaccepted0.2.02022-01-11 07:44:02 UTC782022-10-08 07:54:59 UTC720224236JorisVankerschaverCenter for Biosystems and Biotech Data Analysis, Ghent University Global Campus, Republic of Korea, Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Belgium0000-0002-5813-5659StevenJ.KernEnthought Inc., 200 W Cesar Chavez, Austin, TX 78701, United States0000-0002-3789-7400RobertKernEnthought Inc., 200 W Cesar Chavez, Austin, TX 78701, United States10.21105/joss.04236https://doi.org/10.5281/zenodo.7142747Python, Cython, C++https://joss.theoj.org/papers/10.21105/joss.04236.pdfpython, genomics, bioinformaticstag:joss.theoj.org,2005:Paper/29732022-01-29T00:44:59Z2022-01-30T00:01:17ZBam-readcount - rapid generation of basepair-resolution sequence metricsaccepted1.02021-08-15 14:11:57 UTC692022-01-29 00:44:59 UTC720223722AjayKhannaDivision of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MODavidE.LarsonMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, Current Affiliation: Benson Hill, Inc. St. Louis, MOSridharNonavinkereSrivatsanDivision of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MOMatthewMosiorDivision of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, Current Affiliation: Moffitt Cancer Center, Tampa, FLTravisE.AbbottMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, Current Affiliation: Google, Inc. Mountain View, CASusannaKiwalaMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MOTimothyJ.LeyDivision of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MOEricJ.DuncavageDepartment of Pathology, Washington University School of Medicine, St. Louis, MOMatthewJ.WalterDivision of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MOJasonR.WalkerMcDonnell Genome Institute, Washington University School of Medicine, St. Louis, MOObiL.GriffithDivision of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, Department of Genetics, Washington University School of Medicine, St. Louis, MOMalachiGriffithDivision of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, Department of Genetics, Washington University School of Medicine, St. Louis, MOChristopherA.MillerDivision of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO10.21105/joss.03722https://doi.org/10.5281/zenodo.5879149Rhttps://joss.theoj.org/papers/10.21105/joss.03722.pdfgenomics, cpp, sequencingtag:joss.theoj.org,2005:Paper/25902021-11-27T08:31:41Z2021-11-28T00:00:27ZexperDesign: stratifying samples into batches with minimal biasaccepted0.1.02021-04-23 09:09:11 UTC672021-11-27 08:31:41 UTC620213358LluísRevillaSanchoCentro de Investigación Biomédica en Red, Enfermedades Hepáticas y Digestivas, Institut d’Investigacions Biomèdiques August Pi i Sunyer, IDIBAPS0000-0001-9747-2570Juan-JoséLozanoCentro de Investigación Biomédica en Red, Enfermedades Hepáticas y Digestivas0000-0001-9747-2570AzucenaSalasInstitut d’Investigacions Biomèdiques August Pi i Sunyer, IDIBAPS0000-0001-9747-257010.21105/joss.03358https://doi.org/10.5281/zenodo.5718051Rhttps://joss.theoj.org/papers/10.21105/joss.03358.pdfbatch effect, experiment designtag:joss.theoj.org,2005:Paper/27652021-08-06T21:06:23Z2021-08-07T00:02:19ZCutePeaks: A modern viewer for Sanger trace fileaccepted0.2.32021-06-15 20:05:47 UTC642021-08-06 21:06:23 UTC620213457SachaSchutzCHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, Brest, France, Univ Brest, Inserm, EFS, UMR 1078, GGB, 292000000-0002-4563-7537CharlesMonod-BrocaUniv Brest, Inserm, EFS, UMR 1078, GGB, 292000000-0003-4095-8099Anne-SophieDenommé-PichonUnité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France, UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France0000-0002-8986-822210.21105/joss.03457https://doi.org/10.5281/zenodo.5148809QMake, Inno Setup, C++https://joss.theoj.org/papers/10.21105/joss.03457.pdfPython, Sanger, genetics, Qt, GUItag:joss.theoj.org,2005:Paper/25622021-07-10T07:25:28Z2021-07-11T00:01:31ZmicroViz: an R package for microbiome data visualization and statisticsaccepted0.7.02021-04-09 10:12:46 UTC632021-07-10 07:25:28 UTC620213201DavidJ.m.BarnettMaastricht Centre for Systems Biology (MaCSBio), Maastricht University Medical Center+, Department of Medical Microbiology0000-0003-1961-7206IljaC.w.ArtsMaastricht Centre for Systems Biology (MaCSBio)0000-0001-6462-6692JohnPendersMaastricht University Medical Center+, Department of Medical Microbiology, Maastricht University, Public Health Research Institute (CAPHRI), Maastricht University, School of Nutrition and Translational Research in Metabolism (NUTRIM)0000-0001-9146-591910.21105/joss.03201https://doi.org/10.5281/zenodo.5048013Rhttps://joss.theoj.org/papers/10.21105/joss.03201.pdfmicrobiome, visualization