tag:joss.theoj.org,2005:/papers/edited_by/@pjotrpJournal of Open Source Software2019-04-03T15:30:45ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/8552019-04-03T15:30:45Z2021-02-15T11:32:32Ziced: fast and memory efficient normalization of contact mapsacceptedv0.5.12019-02-11 16:51:44 UTC362019-04-03 15:30:45 UTC420191286NelleVaroquauxUniversity of California, Berkeley0000-0002-8748-6546NicolasServantInstitut Curie, INSERM U900, Mines ParisTech0000-0003-1678-741010.21105/joss.01286https://doi.org/10.5281/zenodo.2622857PowerShell, Pythonhttps://joss.theoj.org/papers/10.21105/joss.01286.pdfHi-C contact count, Normalizationtag:joss.theoj.org,2005:Paper/5602019-04-02T09:29:18Z2021-02-15T11:33:11ZTraitDB: Web application database of phenotypic trait data.acceptedv0.9.12018-07-20 15:46:05 UTC362019-04-02 09:29:18 UTC420191201DanLeehrNational Evolutionary Synthesis Center0000-0003-3221-9579MercedesGosbyNational Evolutionary Synthesis Center10.21105/joss.01201https://doi.org/10.5281/zenodo.2609163Ruby, CoffeeScript, JavaScripthttps://joss.theoj.org/papers/10.21105/joss.01201.pdftrait, rails, csvtag:joss.theoj.org,2005:Paper/8952019-03-28T13:14:39Z2021-02-15T11:32:30Zriskclustr: Functions to Study Etiologic Heterogeneityaccepted0.1.02019-02-18 22:21:54 UTC352019-03-28 13:14:39 UTC420191269EmilyC.ZaborMemorial Sloan Kettering Cancer Center0000-0002-1402-449810.21105/joss.01269https://doi.org/10.5281/zenodo.2612856Rhttps://joss.theoj.org/papers/10.21105/joss.01269.pdfbiostatistics, epidemiology, etiologic heterogeneity, clustering, disease subtypes, multinomial logistic regression, polytomous logistic regressiontag:joss.theoj.org,2005:Paper/9042019-03-26T06:26:04Z2021-02-15T11:32:29ZChiRP: Chinese Restaurant Process Mixtures for Regression and Clusteringaccepted1.0.02019-02-27 04:18:29 UTC352019-03-26 06:26:04 UTC420191287ArmanOganisianDepartment of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania0000-0002-0437-461110.21105/joss.01287https://doi.org/10.5281/zenodo.2591600Rhttps://joss.theoj.org/papers/10.21105/joss.01287.pdfBayesian, Nonparametric, Clustering, Dirichlet Process, Chinese Restauranttag:joss.theoj.org,2005:Paper/2822019-03-13T17:44:10Z2021-02-15T11:33:53ZCytobankAPIstats: Computes Signaling and Population Statistics for Cytometry Data on Cytobank using 'CytobankAPI'acceptedv1.02017-09-18 19:08:18 UTC352019-03-13 17:44:10 UTC42019445AllisonA.ThromDepartment of Biomedical Enginering, Washington University in St. Louis, St. Louis, MO, USA, Department of Pediatrics, Washington University in St. Louis, St. Louis, MO, USA0000-0001-6689-7904AnthonyR.FrenchDepartment of Biomedical Enginering, Washington University in St. Louis, St. Louis, MO, USA, Department of Pediatrics, Washington University in St. Louis, St. Louis, MO, USA0000-0002-4556-839110.21105/joss.00445https://doi.org/10.5281/zenodo.2583300Rhttps://joss.theoj.org/papers/10.21105/joss.00445.pdfmass cytometrytag:joss.theoj.org,2005:Paper/8462019-02-28T14:14:35Z2021-02-15T11:32:33ZpycoQC, interactive quality control for Oxford Nanopore Sequencingacceptedv2.2.02019-02-04 16:10:37 UTC342019-02-28 14:14:35 UTC420191236AdrienLegerEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridgeshire, UK0000-0001-8772-6776TommasoLeonardiGurdon Institute, Cambridge, Cambridgeshire, UK, Center for Genomic Science IIT\@SEMM, Istituto Italiano di Tecnologia (IIT), Milan, Italy0000-0002-4449-186310.21105/joss.01236https://doi.org/10.5281/zenodo.2578275Pythonhttps://joss.theoj.org/papers/10.21105/joss.01236.pdfpython3, plots, metrics, nanopore sequencing, interactive, quality controltag:joss.theoj.org,2005:Paper/7332019-01-25T13:35:55Z2021-02-15T11:32:47Zsierra-local: A lightweight standalone application for drug resistance predictionacceptedv0.1.22018-11-26 16:18:15 UTC332019-01-25 13:35:55 UTC420191186JasperC.HoDepartment of Pathology and Laboratory Medicine, Western University, London, ON, Canada0000-0003-0693-8940GarwayT.NgDepartment of Pathology and Laboratory Medicine, Western University, London, ON, CanadaMathiasRenaudDepartment of Pathology and Laboratory Medicine, Western University, London, ON, CanadaArtF. y.PoonDepartment of Pathology and Laboratory Medicine, Western University, London, ON, Canada, Department of Microbiology and Immunology, Western University, London, ON, Canada, Department of Applied Mathematics, Western University, London, ON, Canada0000-0003-3779-154X10.21105/joss.01186https://doi.org/10.5281/zenodo.2548745Python, Rhttps://joss.theoj.org/papers/10.21105/joss.01186.pdfbioinformatics, HIV/AIDS, drug resistance, sequence analysis, clinical virologytag:joss.theoj.org,2005:Paper/7432019-01-18T11:31:26Z2021-02-15T11:32:45Zswsc: A sitewise UCE partitioneracceptedv6.0.12018-12-04 21:51:58 UTC332019-01-18 11:31:26 UTC420191146RyanA.HagensonOmaha's Henry Doorly Zoo and Aquarium0000-0001-9750-192510.21105/joss.01146https://doi.org/10.5281/zenodo.2542907Gohttps://joss.theoj.org/papers/10.21105/joss.01146.pdfultraconserved elements, partitioning, entropy, gc percentagetag:joss.theoj.org,2005:Paper/3522019-01-05T18:09:32Z2024-01-04T16:33:56ZgenieR: An R package for inference of demographic history of phylogeniesacceptedv1.0.02018-01-16 10:43:30 UTC332019-01-05 18:09:32 UTC42019634FeiXiangDepartment of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom0000-0003-3644-7114BethanyDearloveUS Military HIV Research Program, Rockville, MD, United States0000-0003-3653-4592SimonFrostDepartment of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom0000-0002-5207-987910.21105/joss.00634https://doi.org/10.5281/zenodo.2532305R, C++https://joss.theoj.org/papers/10.21105/joss.00634.pdfdemographic history, phylogeny, coalescent modelstag:joss.theoj.org,2005:Paper/7572019-01-02T17:58:31Z2021-02-15T11:32:43Ztissueloc: Whole slide digital pathology image tissue localizationacceptedv1.0.02018-12-20 18:40:08 UTC332019-01-02 17:58:31 UTC420191148PingjunChenJ. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida0000-0003-0528-1713LinYangJ. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida10.21105/joss.01148https://doi.org/10.5281/zenodo.2529982Pythonhttps://joss.theoj.org/papers/10.21105/joss.01148.pdfwhole slide image, digital pathology, tissue localization, tissue detection, tissue region, pyramid structure