tag:joss.theoj.org,2005:/papers/tagged/data%20pipelineJournal 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/37432022-12-21T19:48:09Z2022-12-22T00:00:50ZPACMAN: A pipeline to reduce and analyze Hubble Wide Field Camera 3 IR Grism dataacceptedv0.1-alpha2022-07-25 15:59:23 UTC802022-12-21 19:48:09 UTC720224838SebastianZiebaMax-Planck-Institut für Astronomie, Königstuhl 17, D-69117 Heidelberg, Germany, Leiden Observatory, Leiden University, Niels Bohrweg 2, 2333CA Leiden, The Netherlands0000-0003-0562-6750LauraKreidbergMax-Planck-Institut für Astronomie, Königstuhl 17, D-69117 Heidelberg, Germany0000-0003-0514-114710.21105/joss.04838https://doi.org/10.5281/zenodo.7465579Pythonhttps://joss.theoj.org/papers/10.21105/joss.04838.pdfHST, python, astronomy, exoplanets, spectroscopy, photometrytag:joss.theoj.org,2005:Paper/36862022-12-13T22:19:24Z2022-12-16T16:04:22Zdtrackr: An R package for tracking the provenance of dataaccepted0.2.32022-06-28 15:30:26 UTC802022-12-13 22:19:24 UTC720224707RobertChallenEngineering Mathematics, University of Bristol, Bristol, United Kingdom, College of Engineering, Mathematics and Physical Sciences, University of Exeter, Devon, United Kingdom0000-0002-5504-776810.21105/joss.04707https://doi.org/10.5281/zenodo.7433514Rhttps://joss.theoj.org/papers/10.21105/joss.04707.pdfdata pipeline, consort diagram, strobe statement, data quality, reproducible researchtag:joss.theoj.org,2005:Paper/25822022-01-29T00:08:44Z2022-01-31T10:50:21ZSenSARP: A pipeline to pre-process Sentinel-1 SLC data by using ESA SNAP Sentinel-1 Toolboxaccepted0.12021-04-20 14:24:27 UTC692022-01-29 00:08:44 UTC720223337ThomasWeißDepartment of Geography, Ludwig-Maximilians-Universität München, 80333 Munich, Germany0000-0001-5278-8379TonioFinckeBrockmann Consult GmbH, 21029 Hamburg, Germany;10.21105/joss.03337https://doi.org/10.5281/zenodo.5903483Pythonhttps://joss.theoj.org/papers/10.21105/joss.03337.pdfSentinel-1, SAR, SNAPtag:joss.theoj.org,2005:Paper/31462022-01-12T22:41:39Z2022-01-23T18:41:48ZVeridicalFlow: a Python package for building trustworthy data science pipelines with PCSacceptedv0.0.22021-11-01 23:30:20 UTC692022-01-12 22:41:39 UTC720223895JamesDuncanStatistics Department, University of California, Berkeley0000-0003-3297-681XRushKapoorEECS Department, University of California, BerkeleyAbhineetAgarwalPhysics Department, University of California, BerkeleyChandanSinghEECS Department, University of California, Berkeley0000-0003-0318-2340BinYuStatistics Department, University of California, Berkeley, EECS Department, University of California, Berkeley10.21105/joss.03895https://doi.org/10.5281/zenodo.5841669Jupyter Notebook, Pythonhttps://joss.theoj.org/papers/10.21105/joss.03895.pdfpython, stability, reproducibility, data science, cachingtag:joss.theoj.org,2005:Paper/30682021-11-27T07:14:35Z2021-11-28T00:00:25ZSNEWPY: A Data Pipeline from Supernova Simulations to Neutrino Signalsacceptedv1.1b32021-09-13 18:33:33 UTC672021-11-27 07:14:35 UTC620213772AmandaL.BaxterPurdue University, West Lafayette, IN, USASegevBenZviUniversity of Rochester, Rochester, NY, USA0000-0001-5537-4710JoahanCastanedaJaimesCalifornia Institute of Technology, Pasadena, CA, USAAlexisColeiroUniversité de Paris, CNRS, AstroParticule et Cosmologie, Paris, FranceMartaColomerMollaUniversité Libre de Bruxelles, Brussels, Belgium0000-0003-1801-8121DamienDornicAix Marseille Univ, CNRS/IN2P3, CPPM, Marseille, FranceSpencerGriswoldUniversity of Rochester, Rochester, NY, USA0000-0002-7321-7513TomerGoldhagenUniversity of North Carolina - Chapel Hill, Chapel Hill, NC, USAAnneGrafNC State University, Raleigh, NC, USAAlecHabigUniversity of Minnesota Duluth, Duluth, MN, USA0000-0002-1018-9383RemingtonHillLaurentian University, Sudbury, ON, CanadaShunsakuHoriuchiVirginia Tech, Blacksburg, VA, USA0000-0001-6142-6556JamesP.KnellerNC State University, Raleigh, NC, USA0000-0002-3502-3830MathieuLamoureuxINFN Sezione di Padova, Padova, Italy0000-0002-8860-5826RafaelF.LangPurdue University, West Lafayette, IN, USA0000-0001-7594-2746MassimilianoLincettoRuhr-Universität Bochum, Bochum, Germany0000-0002-1460-3369JostMigendaKing’s College London, London, UK0000-0002-5350-8049McKenzieMyersNC State University, Raleigh, NC, USA0000-0002-2901-9173EvanO'ConnorStockholm University, Stockholm, SwedenAndrewRenshawUniversity of Houston, Houston, TX, USA0000-0003-2913-8057KateScholbergDuke University, Durham, NC, USA0000-0002-7007-2021AndreySheshukovJoint Institute for Nuclear Research, Dubna, Russia0000-0001-5128-9279JeffTsengOxford University, Oxford, UK0000-0003-1731-5853ChristopherTunnellRice University, Houston, TX, USA0000-0001-8158-7795NavyaUberoiUniversity of Rochester, Rochester, NY, USAArkinWorlikarGeorgia Institute of Technology, Atlanta, GA, USA10.21105/joss.03772https://doi.org/10.5281/zenodo.5719209Jupyter Notebook, Pythonhttps://joss.theoj.org/papers/10.21105/joss.03772.pdfastronomy, supernova, neutrinostag: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/16732020-12-16T19:07:22Z2021-02-15T11:30:41ZPypeIt: The Python Spectroscopic Data Reduction Pipelineacceptedv1.0.32020-05-22 14:55:03 UTC562020-12-16 19:07:22 UTC520202308J.XavierProchaskaUniversity of California, Santa Cruz, Kavli Institute for the Physics and Mathematics of the Universe0000-0002-7738-6875JosephF.HennawiUniversity of California, Santa Barbara0000-0002-7054-4332KyleB.WestfallUniversity of California Observatories0000-0003-1809-6920RyanJ.CookeDurham University, UK0000-0001-7653-5827FeigeWangKavli Institute for the Physics and Mathematics of the Universe, Steward Observatory, University of Arizona0000-0002-7633-431XTiffanyHsyuUniversity of California, Santa Cruz0000-0002-0462-3139FrederickB.DaviesKavli Institute for the Physics and Mathematics of the Universe, Lawrence Berkeley National Laboratory0000-0003-0821-3644EmanuelePaoloFarinaKavli Institute for the Physics and Mathematics of the Universe, Max Planck Institut f\"{u}r Astrophysik0000-0002-6822-2254DeboraPellicciaUniversity of California Observatories0000-0002-3007-001310.21105/joss.02308https://doi.org/10.5281/zenodo.4323006Python, Jupyter Notebook, Chttps://joss.theoj.org/papers/10.21105/joss.02308.pdfastronomy, data reduction, spectroscopytag:joss.theoj.org,2005:Paper/16072020-08-23T00:00:00Z2022-08-25T16:41:55Zdantro: a Python package for handling, transforming, and visualizing hierarchically structured dataacceptedv0.132020-05-20 14:00:10 UTC522020-08-23 00:00:00 UTC520202316YunusSevinchanInstitute of Environmental Physics, Heidelberg University, Germany0000-0003-3858-0904BenjaminHerdeanuInstitute of Environmental Physics, Heidelberg University, Germany, Heidelberg Graduate School for Physics, Heidelberg University, Germany0000-0001-6343-3004JeremiasTraubInstitute of Environmental Physics, Heidelberg University, Germany0000-0001-8911-636510.21105/joss.02316https://doi.org/10.5281/zenodo.3986628Pythonhttps://joss.theoj.org/papers/10.21105/joss.02316.pdfYAML, computer simulations, research software, data analysis, plotting, data processing pipeline, configuration-based interfaces, hierarchical data structures, HDF5tag:joss.theoj.org,2005:Paper/10022019-06-06T14:47:49Z2021-02-15T11:32:10ZA reproducible Snakemake pipeline to analyse Illumina paired-end data from ChiP-Seq experimentsacceptedv1.2.02019-05-17 15:30:39 UTC382019-06-06 14:47:49 UTC420191465JihedChouarefSwammerdam Institute for Life Sciences, University of Amsterdam0000-0003-3865-896XMattijsBliekSwammerdam Institute for Life Sciences, University of Amsterdam0000-0002-0488-4873MarcGallandSwammerdam Institute for Life Sciences, University of Amsterdam0000-0003-2161-868910.21105/joss.01465https://doi.org/10.5281/zenodo.3240026Pythonhttps://joss.theoj.org/papers/10.21105/joss.01465.pdfSnakemake, ChIP-seq, Deeptools, Bioconda