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Tytuł:
CITEViz: interactively classify cell populations in CITE-Seq via a flow cytometry-like gating workflow using R-Shiny.
Autorzy:
Kong GL; Division of Oncologic Sciences, Knight Cancer Institute, Oregon Health and Science University, 3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, OR, 97239, USA.
Nguyen TT; Division of Oncologic Sciences, Knight Cancer Institute, Oregon Health and Science University, 3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, OR, 97239, USA.
Rosales WK; Earle A. Chiles Research Institute, Providence, Portland, OR, 97213, USA.
Panikar AD; Knight Campus Graduate Internship Program - Bioinformatics, University of Oregon, Eugene, OR, 97403, USA.
Cheney JHW; Knight Campus Graduate Internship Program - Bioinformatics, University of Oregon, Eugene, OR, 97403, USA.
Lusardi TA; Cancer Early Detection Advanced Research, Oregon Health and Science University, Portland, OR, 97238, USA.
Yashar WM; Division of Oncologic Sciences, Knight Cancer Institute, Oregon Health and Science University, 3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, OR, 97239, USA.; Department of Biomedical Engineering, Oregon Health and Science University, Portland, USA.
Curtiss BM; Division of Oncologic Sciences, Knight Cancer Institute, Oregon Health and Science University, 3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, OR, 97239, USA.
Carratt SA; Division of Oncologic Sciences, Knight Cancer Institute, Oregon Health and Science University, 3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, OR, 97239, USA.
Braun TP; Division of Oncologic Sciences, Knight Cancer Institute, Oregon Health and Science University, 3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, OR, 97239, USA. .; Division of Hematology and Medical Oncology, Oregon Health and Science University, Portland, USA. .
Maxson JE; Division of Oncologic Sciences, Knight Cancer Institute, Oregon Health and Science University, 3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, OR, 97239, USA. .
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Źródło:
BMC bioinformatics [BMC Bioinformatics] 2024 Apr 02; Vol. 25 (1), pp. 142. Date of Electronic Publication: 2024 Apr 02.
Typ publikacji:
Journal Article
MeSH Terms:
Software*
Leukocytes, Mononuclear*
Humans ; Sequence Analysis, RNA/methods ; Workflow ; Flow Cytometry ; Membrane Proteins ; Single-Cell Analysis/methods ; Gene Expression Profiling/methods
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
shinyMBA: a novel R shiny application for quality control of the multiplex bead assay for serosurveillance studies.
Autorzy:
Matson Z; Viral Vaccine Preventable Diseases Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA. .
Cooley G; Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA.
Parameswaran N; Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA.
Simon A; Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA.
Bankamp B; Viral Vaccine Preventable Diseases Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
Coughlin MM; Laboratory Branch, Coronavirus and Other Respiratory Viruses Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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Źródło:
Scientific reports [Sci Rep] 2024 Mar 28; Vol. 14 (1), pp. 7442. Date of Electronic Publication: 2024 Mar 28.
Typ publikacji:
Journal Article
MeSH Terms:
Software*
Seroepidemiologic Studies ; Quality Control ; Reference Standards ; Workflow
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Sensor extended imaging workflow for creating fit for purpose models in basic and applied cell biology.
Autorzy:
Schueler J; Charles River Germany GmbH, Am Flughafen 12-14, 79111, Freiburg, Germany. .
Sjöman H; Vitroscope AS, Leirfossvegen 5d, 7037, Trondheim, Norway.
Kriesi C; Vitroscope AS, Leirfossvegen 5d, 7037, Trondheim, Norway.
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Źródło:
Communications biology [Commun Biol] 2024 Feb 10; Vol. 7 (1), pp. 170. Date of Electronic Publication: 2024 Feb 10.
Typ publikacji:
Journal Article; Review
MeSH Terms:
Software*
Diagnostic Imaging*
Humans ; Workflow
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Kuura-An automated workflow for analyzing WES and WGS data.
Autorzy:
Jambulingam D; Institute of Biomedicine, Cancer Research Unit and FICAN West Cancer Centre, University of Turku and Turku University Hospital, Turku, Finland.
Rathinakannan VS; Institute of Biomedicine, Cancer Research Unit and FICAN West Cancer Centre, University of Turku and Turku University Hospital, Turku, Finland.
Heron S; Institute of Biomedicine, Cancer Research Unit and FICAN West Cancer Centre, University of Turku and Turku University Hospital, Turku, Finland.
Schleutker J; Institute of Biomedicine, Cancer Research Unit and FICAN West Cancer Centre, University of Turku and Turku University Hospital, Turku, Finland.; Department of Genomics, Laboratory Division, Turku University Hospital, Turku, Finland.
Fey V; Institute of Biomedicine, Cancer Research Unit and FICAN West Cancer Centre, University of Turku and Turku University Hospital, Turku, Finland.; Faculty of Medicine and Health Technology/BioMediTech, Tampere University, Tampere, Finland.
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Źródło:
PloS one [PLoS One] 2024 Jan 18; Vol. 19 (1), pp. e0296785. Date of Electronic Publication: 2024 Jan 18 (Print Publication: 2024).
Typ publikacji:
Journal Article
MeSH Terms:
Computational Biology*/methods
Software*
Workflow ; Reproducibility of Results ; Whole Genome Sequencing
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
kGWASflow: a modular, flexible, and reproducible Snakemake workflow for k-mers-based GWAS.
Autorzy:
Corut AK; Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
Wallace JG; Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.; Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, GA 30602, USA.; Department of Crop and Soil Sciences, University of Georgia, Athens, GA 30602, USA.
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Źródło:
G3 (Bethesda, Md.) [G3 (Bethesda)] 2023 Dec 29; Vol. 14 (1).
Typ publikacji:
Journal Article
MeSH Terms:
Software*
Genome-Wide Association Study*
Workflow ; Reproducibility of Results ; Phenotype
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
BioMOBS: A multi-omics visual analytics workflow for biomolecular insight generation.
Autorzy:
Heylen D; Theory Lab, Data Science Institute (DSI), Hasselt University, Diepenbeek, Belgium.; Flemish Institute for Technological Research (VITO), Mol, Belgium.
Peeters J; Data Science Institute (DSI), Hasselt University, Diepenbeek, Belgium.
Aerts J; Visual Data Analysis Lab, Department of Biostystems KU Leuven, Leuven, Belgium.
Ertaylan G; Flemish Institute for Technological Research (VITO), Mol, Belgium.
Hooyberghs J; Theory Lab, Data Science Institute (DSI), Hasselt University, Diepenbeek, Belgium.
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Źródło:
PloS one [PLoS One] 2023 Dec 14; Vol. 18 (12), pp. e0295361. Date of Electronic Publication: 2023 Dec 14 (Print Publication: 2023).
Typ publikacji:
Journal Article
MeSH Terms:
Software*
Diabetes Mellitus, Type 2*
Humans ; Multiomics ; Workflow
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Transformer-based tool recommendation system in Galaxy.
Autorzy:
Kumar A; Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110, Freiburg, Germany. .
Grüning B; Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110, Freiburg, Germany.
Backofen R; Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110, Freiburg, Germany.; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schaenzlestr. 18, 79104, Freiburg, Germany.
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Źródło:
BMC bioinformatics [BMC Bioinformatics] 2023 Nov 27; Vol. 24 (1), pp. 446. Date of Electronic Publication: 2023 Nov 27.
Typ publikacji:
Journal Article
MeSH Terms:
Software*
Neural Networks, Computer*
Workflow ; Data Analysis ; Europe
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Facilitating bioinformatics reproducibility with QIIME 2 Provenance Replay.
Autorzy:
Keefe CR; Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America.
Dillon MR; Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America.
Gehret E; Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America.
Herman C; Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America.; School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America.
Jewell M; Department of Epidemiology, University of Washington, Seattle, Washington, United States of America.
Wood CV; Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America.
Bolyen E; Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America.
Caporaso JG; Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, United States of America.; School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America.
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Źródło:
PLoS computational biology [PLoS Comput Biol] 2023 Nov 27; Vol. 19 (11), pp. e1011676. Date of Electronic Publication: 2023 Nov 27 (Print Publication: 2023).
Typ publikacji:
Journal Article
MeSH Terms:
Computational Biology*/methods
Software*
Reproducibility of Results ; Workflow
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Asterics: a simple tool for the ExploRation and Integration of omiCS data.
Autorzy:
Maigné É; Université de Toulouse, INRAE, UR MIAT, 31326, Castanet-Tolosan, France.
Noirot C; Université de Toulouse, INRAE, UR MIAT, 31326, Castanet-Tolosan, France.; Université Fédérale de Toulouse, INRAE, Bioinfomics, Genotoul Bioinformatics Facility, 31326, Castanet-Tolosan, France.
Henry J; Université de Toulouse, INRAE, UR MIAT, 31326, Castanet-Tolosan, France.; Plateforme Biostatistique, Genotoul, Toulouse, France.
Adu Kesewaah Y; Université de Toulouse, INRAE, UR MIAT, 31326, Castanet-Tolosan, France.; Plateforme Biostatistique, Genotoul, Toulouse, France.
Badin L; Hyphen-Stat, Toulouse, France.
Déjean S; Plateforme Biostatistique, Genotoul, Toulouse, France.; IMT, UMR 5219, Université de Toulouse, CNRS, UPS, 31062, Toulouse, France.
Guilmineau C; Université de Toulouse, INRAE, UR MIAT, 31326, Castanet-Tolosan, France.; Plateforme Biostatistique, Genotoul, Toulouse, France.
Krebs A; Université de Toulouse, INRAE, UR MIAT, 31326, Castanet-Tolosan, France.; Université Fédérale de Toulouse, INRAE, Bioinfomics, Genotoul Bioinformatics Facility, 31326, Castanet-Tolosan, France.
Mathevet F; Université de Toulouse, INRAE, UR MIAT, 31326, Castanet-Tolosan, France.; Plateforme Biostatistique, Genotoul, Toulouse, France.
Segalini A; Hyphen-Stat, Toulouse, France.
Thomassin L; Hyphen-Stat, Toulouse, France.
Colongo D; Hyphen-Stat, Toulouse, France.
Gaspin C; Université de Toulouse, INRAE, UR MIAT, 31326, Castanet-Tolosan, France.; Université Fédérale de Toulouse, INRAE, Bioinfomics, Genotoul Bioinformatics Facility, 31326, Castanet-Tolosan, France.
Liaubet L; GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France.
Vialaneix N; Université de Toulouse, INRAE, UR MIAT, 31326, Castanet-Tolosan, France. .; Plateforme Biostatistique, Genotoul, Toulouse, France. .
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Źródło:
BMC bioinformatics [BMC Bioinformatics] 2023 Oct 18; Vol. 24 (1), pp. 391. Date of Electronic Publication: 2023 Oct 18.
Typ publikacji:
Journal Article
MeSH Terms:
Software*
Workflow
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Using machine learning surrogate modeling for faster QSP VP cohort generation.
Autorzy:
Myers RC; Rosa & Co, San Carlos, California, USA.
Augustin F; The MathWorks Inc, Natick, Massachusetts, USA.
Huard J; The MathWorks GmbH, Munich, Germany.
Friedrich CM; Rosa & Co, San Carlos, California, USA.
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Źródło:
CPT: pharmacometrics & systems pharmacology [CPT Pharmacometrics Syst Pharmacol] 2023 Aug; Vol. 12 (8), pp. 1047-1059. Date of Electronic Publication: 2023 Jun 16.
Typ publikacji:
Journal Article
MeSH Terms:
Network Pharmacology*
Software*
Humans ; Uncertainty ; Workflow
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Research on Lightweight Microservice Composition Technology in Cloud-Edge Device Scenarios.
Autorzy:
Li H; School of Electronics and Information Engineering, Tongji University, Shanghai 200092, China.
Liu X; School of Electronics and Information Engineering, Tongji University, Shanghai 200092, China.
Zhao W; School of Electronics and Information Engineering, Tongji University, Shanghai 200092, China.
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Źródło:
Sensors (Basel, Switzerland) [Sensors (Basel)] 2023 Jun 26; Vol. 23 (13). Date of Electronic Publication: 2023 Jun 26.
Typ publikacji:
Journal Article
MeSH Terms:
Software*
Technology*
Workflow
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Tidyproteomics: an open-source R package and data object for quantitative proteomics post analysis and visualization.
Autorzy:
Jones J; Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, 91125, USA. .; Division of Physics, Mathematics and Astronomy, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA. .
MacKrell EJ; Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA.
Wang TY; Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, 91125, USA.
Lomenick B; Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, 91125, USA.
Roukes ML; Division of Physics, Mathematics and Astronomy, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA.
Chou TF; Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, CA, 91125, USA.; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
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Źródło:
BMC bioinformatics [BMC Bioinformatics] 2023 Jun 06; Vol. 24 (1), pp. 239. Date of Electronic Publication: 2023 Jun 06.
Typ publikacji:
Journal Article
MeSH Terms:
Proteomics*/methods
Software*
Algorithms ; Mass Spectrometry/methods ; Workflow
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Scikick: A sidekick for workflow clarity and reproducibility during extensive data analysis.
Autorzy:
Carlucci M; The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.; Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
Bareikis T; The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.; Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
Koncevičius K; Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
Gibas P; The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.; Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
Kriščiūnas A; Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
Petronis A; The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.; Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
Oh G; The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.; Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.; Stanford University School of Medicine, Stanford, California, United States of America.
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Źródło:
PloS one [PLoS One] 2023 Jul 27; Vol. 18 (7), pp. e0289171. Date of Electronic Publication: 2023 Jul 27 (Print Publication: 2023).
Typ publikacji:
Journal Article
MeSH Terms:
Computational Biology*/methods
Software*
Workflow ; Reproducibility of Results ; Data Analysis
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Accelerating genomic workflows using NVIDIA Parabricks.
Autorzy:
O'Connell KA; Health Data and AI, Deloitte Consulting LLP, VA, 22009, Arlington, USA.
Yosufzai ZB; Health Data and AI, Deloitte Consulting LLP, VA, 22009, Arlington, USA.
Campbell RA; Health Data and AI, Deloitte Consulting LLP, VA, 22009, Arlington, USA.
Lobb CJ; Health Data and AI, Deloitte Consulting LLP, VA, 22009, Arlington, USA.
Engelken HT; Health Data and AI, Deloitte Consulting LLP, VA, 22009, Arlington, USA.
Gorrell LM; Health Data and AI, Deloitte Consulting LLP, VA, 22009, Arlington, USA.
Carlson TB; Cloud Managed Services, Deloitte Consulting LLP, Detroit, MI, 48226, USA.
Catana JJ; Health Data and AI, Deloitte Consulting LLP, VA, 22009, Arlington, USA.
Mikdadi D; Health Data and AI, Deloitte Consulting LLP, VA, 22009, Arlington, USA.
Bonazzi VR; Health Data and AI, Deloitte Consulting LLP, VA, 22009, Arlington, USA. .
Klenk JA; Health Data and AI, Deloitte Consulting LLP, VA, 22009, Arlington, USA. .
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Źródło:
BMC bioinformatics [BMC Bioinformatics] 2023 May 31; Vol. 24 (1), pp. 221. Date of Electronic Publication: 2023 May 31.
Typ publikacji:
Journal Article
MeSH Terms:
Computer Graphics*
Software*
Workflow ; Genomics
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Fast all versus all genotype comparison using DNA/RNA sequencing data: method and workflow.
Autorzy:
Eschrich SA; Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
Yu X; Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
Teer JK; Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA. .
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Źródło:
BMC bioinformatics [BMC Bioinformatics] 2023 Apr 24; Vol. 24 (1), pp. 164. Date of Electronic Publication: 2023 Apr 24.
Typ publikacji:
Journal Article
MeSH Terms:
Software*
High-Throughput Nucleotide Sequencing*/methods
Humans ; Workflow ; Genotype ; Sequence Analysis, RNA/methods ; DNA ; Sequence Analysis, DNA/methods
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
A Highly Efficient Workflow for Detecting and Identifying Sequence Variants in Therapeutic Proteins with a High Resolution LC-MS/MS Method.
Autorzy:
Cadang L; Pharma Technical Development, Genentech, South San Francisco, CA 94080, USA.
Tam CYJ; Pharma Technical Development, Genentech, South San Francisco, CA 94080, USA.
Moore BN; Pharma Technical Development, Genentech, South San Francisco, CA 94080, USA.
Fichtl J; Pharma Technical Development, Roche Diagnostics GmbH, 82377 Penzberg, Germany.
Yang F; Pharma Technical Development, Genentech, South San Francisco, CA 94080, USA.
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Źródło:
Molecules (Basel, Switzerland) [Molecules] 2023 Apr 12; Vol. 28 (8). Date of Electronic Publication: 2023 Apr 12.
Typ publikacji:
Journal Article
MeSH Terms:
Tandem Mass Spectrometry*/methods
Software*
Workflow ; Chromatography, Liquid/methods ; High-Throughput Nucleotide Sequencing
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
PSReliP: an integrated pipeline for analysis and visualization of population structure and relatedness based on genome-wide genetic variant data.
Autorzy:
Solovieva E; Research Center for Advanced Analysis, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan.
Sakai H; Research Center for Advanced Analysis, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan. .
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Źródło:
BMC bioinformatics [BMC Bioinformatics] 2023 Apr 05; Vol. 24 (1), pp. 135. Date of Electronic Publication: 2023 Apr 05.
Typ publikacji:
Journal Article
MeSH Terms:
Genome-Wide Association Study*/methods
Software*
Animals ; Genomics/methods ; Genome ; Workflow
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Assessing resource use: a case study with the Human Disease Ontology.
Autorzy:
Baron JA; University of Maryland School of Medicine, Institute for Genome Sciences, 670 W. Baltimore St., HSFIII, Baltimore, MD 21201, USA.
Schriml LM; University of Maryland School of Medicine, Institute for Genome Sciences, 670 W. Baltimore St., HSFIII, Baltimore, MD 21201, USA.
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Źródło:
Database : the journal of biological databases and curation [Database (Oxford)] 2023 Feb 28; Vol. 2023.
Typ publikacji:
Journal Article; Research Support, N.I.H., Extramural
MeSH Terms:
Genomics*
Software*
Humans ; Databases, Factual ; Workflow
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknieSzczegóły
Tytuł:
scAN1.0: A reproducible and standardized pipeline for processing 10X single cell RNAseq data.
Autorzy:
Lepetit M; ENS de Lyon, CNRS UMR 5239, Laboratory of Biology and Modelling of the Cell, Lyon, France.
Ilie MD; Centre de Recherche en Cancérologie (CRCL) - INSERM 1052 - CNRS 5286 - Centre Léon Bérard - Université Claude Bernard Lyon 1, Institut Convergence Plascan, Lyon, France.; Endocrinology Department, 'C.I.Parhon' National Institute of Endocrinology, Bucharest, Romania.
Chanal M; Centre de Recherche en Cancérologie (CRCL) - INSERM 1052 - CNRS 5286 - Centre Léon Bérard - Université Claude Bernard Lyon 1, Institut Convergence Plascan, Lyon, France.
Raverot G; Centre de Recherche en Cancérologie (CRCL) - INSERM 1052 - CNRS 5286 - Centre Léon Bérard - Université Claude Bernard Lyon 1, Institut Convergence Plascan, Lyon, France.; Endocrinology Department, Reference Center for Rare Pituitary Diseases HYPO, 'Groupement Hospitalier Est' Hospices Civils de Lyon, Bron, France.
Bertolino P; Centre de Recherche en Cancérologie (CRCL) - INSERM 1052 - CNRS 5286 - Centre Léon Bérard - Université Claude Bernard Lyon 1, Institut Convergence Plascan, Lyon, France.
Arpin C; ENS de Lyon, CNRS UMR 5239, Laboratory of Biology and Modelling of the Cell, Lyon, France.
Picard F; ENS de Lyon, CNRS UMR 5239, Laboratory of Biology and Modelling of the Cell, Lyon, France.
Gandrillon O; ENS de Lyon, CNRS UMR 5239, Laboratory of Biology and Modelling of the Cell, Lyon, France.; Inria Center Grenoble Rhone-Alpes, Equipe Dracula, Villeurbanne, France.
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Źródło:
In silico biology [In Silico Biol] 2023; Vol. 15 (1-2), pp. 11-21.
Typ publikacji:
Journal Article
MeSH Terms:
RNA-Seq*
Single-Cell Gene Expression Analysis*
Software*
Datasets as Topic ; Humans ; Animals ; Mice ; Pituitary Neoplasms/genetics ; CD8-Positive T-Lymphocytes ; Gene Expression Profiling ; Computational Biology ; Workflow
Czasopismo naukowe
Pełny tekst  Link otwiera się w nowym oknie Pełny tekstSzczegóły
Tytuł:
Design considerations for workflow management systems use in production genomics research and the clinic.
Autorzy:
Ahmed AE; Faculty of Science, Center for Bioinformatics and Systems Biology, University of Khartoum, 11111, Khartoum, Sudan. .; Department of Electrical and Electronic Engineering, Faculty of Engineering, University of Khartoum, 11111, Khartoum, Sudan. .; Bernoulli Institute, University of Groningen, 9747 AG, Groningen, The Netherlands. .
Allen JM; National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
Bhat T; National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.; Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.; Department of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
Burra P; National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.; Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.; Center for Computational Biology, University of California, Berkeley, CA, 94720, USA.
Fliege CE; National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
Hart SN; Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.
Heldenbrand JR; National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
Hudson ME; National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.; Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
Istanto DD; Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
Kalmbach MT; Department of Information Technology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA.
Kapraun GD; Department of Information Technology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA.
Kendig KI; National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
Kendzior MC; National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.; Department of Information Technology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA.
Klee EW; Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.
Mattson N; Department of Information Technology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA.
Ross CA; Laboratory Pathology and Extramural Applications, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA.
Sharif SM; Department of Electrical and Electronic Engineering, Faculty of Engineering, University of Khartoum, 11111, Khartoum, Sudan.
Venkatakrishnan R; National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
Fadlelmola FM; Faculty of Science, Center for Bioinformatics and Systems Biology, University of Khartoum, 11111, Khartoum, Sudan.
Mainzer LS; National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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Źródło:
Scientific reports [Sci Rep] 2021 Nov 04; Vol. 11 (1), pp. 21680. Date of Electronic Publication: 2021 Nov 04.
Typ publikacji:
Comparative Study; Journal Article; Research Support, N.I.H., Extramural
MeSH Terms:
Software*
Workflow*
Computational Biology/*methods
Big Data ; Genomics ; Humans ; Reproducibility of Results
Czasopismo naukowe
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