tag:joss.theoj.org,2005:/papers/reviewed_by/@rcannoodJournal of Open Source Software2023-10-19T10:05:08ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/42982023-10-19T10:05:08Z2023-10-20T00:00:55ZBaargin: a Nextflow workflow for the automatic analysis of bacterial genomics data with a focus on Antimicrobial Resistanceacceptedv0.12023-03-10 09:09:20 UTC902023-10-19 10:05:08 UTC820235397JulietteHayerMIVEGEC, University of Montpellier, IRD, CNRS, 34394, Montpellier, France, Laboratoire Mixte International Drug Resistance in Southeast Asia0000-0003-4899-9637JacquesDainatMIVEGEC, University of Montpellier, IRD, CNRS, 34394, Montpellier, France0000-0002-6629-0173EllaMarcyMIVEGEC, University of Montpellier, IRD, CNRS, 34394, Montpellier, France, Centre Hospitalier Universitaire (CHU) Lapeyronie, Montpellier, France0009-0002-6000-1665Anne-LaureBañulsMIVEGEC, University of Montpellier, IRD, CNRS, 34394, Montpellier, France, Laboratoire Mixte International Drug Resistance in Southeast Asia0000-0002-2106-866710.21105/joss.05397https://doi.org/10.5281/zenodo.8386399Python, Nextflowhttps://joss.theoj.org/papers/10.21105/joss.05397.pdfWhole Genome Shotgun, Genomics, Long reads sequencing technology, Short reads sequencing technology, Antimicrobial Resistance, Pangenometag:joss.theoj.org,2005:Paper/36722022-11-29T10:06:05Z2022-11-30T00:01:31ZALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysisaccepted1.0.42022-06-23 10:57:14 UTC792022-11-29 10:06:05 UTC720224677HåkonKaspersenNorwegian Veterinary Institute, Ås, Norway0000-0002-9559-1303EveZeylFiskebeckNorwegian Veterinary Institute, Ås, Norway0000-0002-6858-197810.21105/joss.04677https://doi.org/10.5281/zenodo.7331351R, Nextflowhttps://joss.theoj.org/papers/10.21105/joss.04677.pdfPhylogeny, Prokaryote, Clusteringtag:joss.theoj.org,2005:Paper/36472022-07-06T15:37:27Z2022-07-07T00:01:02Zstacks: Stacked Ensemble Modeling with Tidy Data Principlesacceptedv0.2.32022-06-08 16:51:58 UTC752022-07-06 15:37:27 UTC720224471SimonP.CouchRStudio PBC0000-0001-5676-5107MaxKuhnRStudio PBC10.21105/joss.04471https://doi.org/10.5281/zenodo.6800026Rhttps://joss.theoj.org/papers/10.21105/joss.04471.pdfdata science, tidyverse, model stacking, ensemblingtag:joss.theoj.org,2005:Paper/25922021-07-20T20:06:25Z2021-07-21T00:03:14ZCollaborative Container Modules with Singularity Registry HPCaccepted0.0.222021-04-24 00:44:09 UTC632021-07-20 20:06:25 UTC620213311VanessaSochatLawrence Livermore National Lab, Livermore, CA, USA0000-0002-4387-3819AlecScottUniversity of Arizona Research Computing, Tuscon, AZ, USA0000-0001-6255-130810.21105/joss.03311https://doi.org/10.5281/zenodo.5116598Tcl, Python, Luahttps://joss.theoj.org/papers/10.21105/joss.03311.pdfcontainers, singularity, linux, registrytag:joss.theoj.org,2005:Paper/17062020-08-21T07:17:25Z2021-02-15T11:30:35Ztidyfst: Tidy Verbs for Fast Data Manipulationacceptedv0.9.72020-06-02 08:42:13 UTC522020-08-21 07:17:25 UTC520202388Tian-YuanHuangSchool of Life Science, Fudan University0000-0002-4151-3764BinZhaoSchool of Life Science, Fudan University0000-0002-3530-246910.21105/joss.02388https://doi.org/10.5281/zenodo.3970861R, Rebolhttps://joss.theoj.org/papers/10.21105/joss.02388.pdfdata.table, data aggregation, data manipulation, dplyr, tidyfsttag:joss.theoj.org,2005:Paper/15342020-07-09T00:33:17Z2021-02-15T11:30:56Zgraphsim: An R package for simulating gene expression data from graph structures of biological pathwaysaccepted0.1.22020-03-02 07:37:42 UTC512020-07-09 00:33:17 UTC520202161S.ThomasKellyDepartment of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
, RIKEN Center for Integrative Medical Sciences, Suehiro-cho-1-7-22, Tsurumi Ward, Yokohama, Kanagawa 230-0045, Japan0000-0003-3904-6690MichaelA.BlackDepartment of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand0000-0003-1174-605410.21105/joss.02161https://doi.org/10.5281/zenodo.3931288R, Rubyhttps://joss.theoj.org/papers/10.21105/joss.02161.pdfgene-expression, simulation, genomics, pathway, networktag:joss.theoj.org,2005:Paper/15152020-03-09T19:33:00Z2021-02-15T11:30:59ZMaterialNet: A web-based graph explorer for materials science dataaccepted1.0.02020-02-13 14:28:49 UTC472020-03-09 19:33:00 UTC520202105RoniChoudhuryKitware Inc.MuratahanAykolToyota Research InstituteSamuelGratzlKitware Inc.JosephMontoyaToyota Research InstituteJensHummelshøjToyota Research Institute10.21105/joss.02105https://doi.org/10.5281/zenodo.3701759JavaScript, Jupyter Notebook, Pythonhttps://joss.theoj.org/papers/10.21105/joss.02105.pdfmaterials science, graph visualization