tag:joss.theoj.org,2005:/papers/tagged/stanJournal of Open Source Software2023-11-06T16:28:16ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/46062023-11-06T16:28:16Z2023-11-07T00:00:17Zmeasr: Bayesian psychometric measurement using Stanacceptedv0.3.12023-07-14 20:06:08 UTC912023-11-06 16:28:16 UTC820235742W.JakeThompsonAccessible, Teaching, Learning, and Assessment Systems, University of Kansas0000-0001-7339-030010.21105/joss.05742https://doi.org/10.5281/zenodo.10058365R, Stan, C++https://joss.theoj.org/papers/10.21105/joss.05742.pdfbayesian-modeling, educational-assessment, psychometrics, diagnostic-modelingtag:joss.theoj.org,2005:Paper/41612023-07-22T03:05:19Z2023-07-23T00:01:35ZBridgeStan: Efficient in-memory access to the methods of a Stan modelacceptedv.1.0.02023-01-10 21:55:16 UTC872023-07-22 03:05:19 UTC820235236EdwardA.RoualdesCalifornia State University, Chico0000-0002-8757-3463BrianWardCenter for Computational Mathematics, Flatiron Institute0000-0002-9841-3342BobCarpenterCenter for Computational Mathematics, Flatiron Institute0000-0002-2433-9688AdrianSeyboldtPyMC Labs0000-0002-4239-4541SethD.AxenCluster of Excellence Machine Learning: New Perspectives for Science, University of Tübingen0000-0003-3933-824710.21105/joss.05236https://doi.org/10.5281/zenodo.8169248R, C, Juliahttps://joss.theoj.org/papers/10.21105/joss.05236.pdfStan, Python, Rust, C++, automatic differentiationtag:joss.theoj.org,2005:Paper/39252022-11-27T23:05:44Z2022-11-28T00:00:56Zbmiptools: BioMaterials Image Processing Toolsaccepted1.0.12022-09-26 09:12:10 UTC792022-11-27 23:05:44 UTC720224859LucaCurcuraciMax-Planck Institute of collodis and interfaces, Potsdam, GermanyRichardWeinkamerMax-Planck Institute of collodis and interfaces, Potsdam, GermanyLucaBertinettiB CUBE - Center for Molecular Bioengineering -Technische Universität Dresden, Germany10.21105/joss.04859https://doi.org/10.5281/zenodo.7337808Pythonhttps://joss.theoj.org/papers/10.21105/joss.04859.pdfimage-processing, scanning electron microscope, FIB-SEM, cryo FIB-SEM, biology, biomaterialstag:joss.theoj.org,2005:Paper/37202022-09-05T10:35:12Z2022-09-06T00:01:06ZSpmImage Tycoon: Organize and analyze scanning probe microscopy dataaccepted0.3.62022-07-14 11:55:54 UTC772022-09-05 10:35:12 UTC720224644AlexanderRissTechnical University of Munich, Physics Department E20, 85748 Garching, Germany0000-0002-3212-792510.21105/joss.04644https://doi.org/10.5281/zenodo.7038825AutoHotkeyhttps://joss.theoj.org/papers/10.21105/joss.04644.pdfJulia, scanning probe microscopy, scanning probe spectroscopy, scanning tunneling microscopy, scanning tunneling spectroscopy, atomic force microscopy, SPM, STM, AFMtag:joss.theoj.org,2005:Paper/26102021-08-14T06:34:52Z2021-08-15T00:01:56ZImSwitch: Generalizing microscope control in Pythonacceptedv1.0.02021-04-30 12:57:02 UTC642021-08-14 06:34:52 UTC620213394XavierCasasMorenoSciLifeLab, KTH Royal Institute of Technology0000-0002-9583-9022StaffanAl-KadhimiSciLifeLab, KTH Royal Institute of Technology0000-0002-3488-6845JonatanAlvelidSciLifeLab, KTH Royal Institute of Technology0000-0002-3554-9322AndreasBodénSciLifeLab, KTH Royal Institute of Technology0000-0001-9302-7576IlariaTestaSciLifeLab, KTH Royal Institute of Technology0000-0003-4005-499710.21105/joss.03394https://doi.org/10.5281/zenodo.5196462Pythonhttps://joss.theoj.org/papers/10.21105/joss.03394.pdfFluorescence microscopy, Super-resolution, Scanning microscopy, Microscope automationtag:joss.theoj.org,2005:Paper/28042021-08-08T13:54:05Z2021-08-09T00:02:17Zbmgarch: An R-Package for Bayesian Multivariate GARCH modelsacceptedv1.0.12021-06-19 03:59:32 UTC642021-08-08 13:54:05 UTC620213452PhilippeRastUniversity of California, Davis0000-0003-3630-6629StephenR.MartinComscore, Inc.0000-0001-8085-239010.21105/joss.03452https://doi.org/10.5281/zenodo.5168675R, Emacs Lisp, C++, Stanhttps://joss.theoj.org/papers/10.21105/joss.03452.pdfstan, GARCHtag:joss.theoj.org,2005:Paper/25772021-04-21T06:09:36Z2021-04-22T00:02:20ZThe stantargets R package: a workflow framework for efficient reproducible Stan-powered Bayesian data analysis pipelinesaccepted0.0.0.90032021-04-15 16:07:03 UTC602021-04-21 06:09:36 UTC620213193WilliamMichaelLandauEli Lilly and Company0000-0003-1878-325310.21105/joss.03193https://doi.org/10.5281/zenodo.4706113R, Stanhttps://joss.theoj.org/papers/10.21105/joss.03193.pdfreproducibility, high-performance computing, pipeline, workflow, Make, Bayesiantag:joss.theoj.org,2005:Paper/17042020-08-17T05:57:27Z2021-02-15T11:30:35Zdms-view: Interactive visualization tool for deep mutational scanning dataacceptedv1.0.02020-06-01 21:39:22 UTC522020-08-17 05:57:27 UTC520202353SarahK.HiltonDivision of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA, Department of Genome Sciences, University of Washington, Seattle, WA, USA0000-0001-9278-3644JohnHuddlestonVaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA, Molecular and Cell Biology, University of Washington, Seattle, WA, USA0000-0002-4250-2063AllisonBlackVaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA, Department of Epidemiology, University of Washington, Seattle, WA, USA0000-0002-6618-4127KhrystynaNorthDivision of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA, Department of Genome Sciences, University of Washington, Seattle, WA, USAAdamS.DingensDivision of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA0000-0001-9603-9409TrevorBedfordVaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA0000-0002-4039-5794JesseD.BloomDivision of Basic Sciences and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA, Department of Genome Sciences, University of Washington, Seattle, WA, USA, Howard Hughes Medical Institute, Seattle, WA, USA0000-0003-1267-340810.21105/joss.02353https://doi.org/10.5281/zenodo.3986155Ruby, JavaScript, Pythonhttps://joss.theoj.org/papers/10.21105/joss.02353.pdfJavascript, D3, molecular biology, protein evolution, data visualizationtag:joss.theoj.org,2005:Paper/13272020-04-13T15:18:20Z2021-02-15T11:31:23Zampscan: A lightweight Python package for shape analysis of prosthetics and orthoticsacceptedv0.3.02019-11-08 16:44:14 UTC482020-04-13 15:18:20 UTC520202060JoshuaW.SteerBioengineering Sciences Research Group, School of Engineering, Faculty of Engineering and Physical Sciences, University of Southampton0000-0002-6288-1347OliverStocksBioengineering Sciences Research Group, School of Engineering, Faculty of Engineering and Physical Sciences, University of SouthamptonJackParsonsBioengineering Sciences Research Group, School of Engineering, Faculty of Engineering and Physical Sciences, University of SouthamptonPeterR.WorsleyClinical Academic Facility, School of Health Sciences, Faculty of Environment and Life Sciences, University of Southampton0000-0003-0145-5042AlexanderS.DickinsonBioengineering Sciences Research Group, School of Engineering, Faculty of Engineering and Physical Sciences, University of Southampton0000-0002-9647-194410.21105/joss.02060https://doi.org/10.5281/zenodo.3741495Pythonhttps://joss.theoj.org/papers/10.21105/joss.02060.pdfprosthetics, orthotics, scanning, meshes, measurementtag:joss.theoj.org,2005:Paper/13402019-12-11T23:26:26Z2021-02-15T11:31:21Zalignparse: A Python package for parsing complex features from high-throughput long-read sequencingaccepted0.1.02019-11-19 23:52:10 UTC442019-12-11 23:26:26 UTC420191915KatharineH.d.CrawfordBasic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA, Department of Genome Sciences and Medical Scientist Training Program, University of Washington, Seattle, Washington, USA0000-0002-6223-4019JesseD.BloomBasic Sciences and Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA, Howard Hughes Medical Institute, Seattle, Washington, USA0000-0003-1267-340810.21105/joss.01915https://doi.org/10.5281/zenodo.3569587Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.01915.pdfPacBio, deep mutational scanning, single-cell virus sequencing, genomics, sequencing