Your browser doesn't support javascript.
loading
The ENCODE Uniform Analysis Pipelines.
Hitz, Benjamin C; Lee, Jin-Wook; Jolanki, Otto; Kagda, Meenakshi S; Graham, Keenan; Sud, Paul; Gabdank, Idan; Strattan, J Seth; Sloan, Cricket A; Dreszer, Timothy; Rowe, Laurence D; Podduturi, Nikhil R; Malladi, Venkat S; Chan, Esther T; Davidson, Jean M; Ho, Marcus; Miyasato, Stuart; Simison, Matt; Tanaka, Forrest; Luo, Yunhai; Whaling, Ian; Hong, Eurie L; Lee, Brian T; Sandstrom, Richard; Rynes, Eric; Nelson, Jemma; Nishida, Andrew; Ingersoll, Alyssa; Buckley, Michael; Frerker, Mark; Kim, Daniel S; Boley, Nathan; Trout, Diane; Dobin, Alex; Rahmanian, Sorena; Wyman, Dana; Balderrama-Gutierrez, Gabriela; Reese, Fairlie; Durand, Neva C; Dudchenko, Olga; Weisz, David; Rao, Suhas S P; Blackburn, Alyssa; Gkountaroulis, Dimos; Sadr, Mahdi; Olshansky, Moshe; Eliaz, Yossi; Nguyen, Dat; Bochkov, Ivan; Shamim, Muhammad Saad.
Afiliación
  • Hitz BC; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
  • Lee JW; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
  • Jolanki O; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
  • Kagda MS; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
  • Graham K; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
  • Sud P; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
  • Gabdank I; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
  • Strattan JS; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
  • Sloan CA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
  • Dreszer T; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
  • Rowe LD; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
  • Podduturi NR; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
  • Malladi VS; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
  • Chan ET; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
  • Davidson JM; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
  • Ho M; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
  • Miyasato S; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
  • Simison M; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
  • Tanaka F; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
  • Luo Y; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
  • Whaling I; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
  • Hong EL; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
  • Lee BT; Genomics Institute, School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA.
  • Sandstrom R; Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA.
  • Rynes E; Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA.
  • Nelson J; Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA.
  • Nishida A; Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA.
  • Ingersoll A; Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA.
  • Buckley M; Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA.
  • Frerker M; Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, 6th Floor, Seattle, WA 98121, USA.
  • Kim DS; Department of Genetics, Department of Computer Science, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94304, USA.
  • Boley N; Department of Genetics, Department of Computer Science, Stanford University, 240 Pasteur Drive, Palo Alto, CA 94304, USA.
  • Trout D; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125 USA.
  • Dobin A; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
  • Rahmanian S; Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA.
  • Wyman D; Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA.
  • Balderrama-Gutierrez G; Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA.
  • Reese F; Center for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA.
  • Durand NC; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
  • Dudchenko O; The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
  • Weisz D; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA.
  • Rao SSP; Department of Computer Science, Rice University, Houston, TX 77030, USA.
  • Blackburn A; The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
  • Gkountaroulis D; The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
  • Sadr M; The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
  • Olshansky M; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
  • Eliaz Y; Department of Medicine, University of California San Francisco, San Francisco, CA 94143, USA.
  • Nguyen D; The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
  • Bochkov I; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA.
  • Shamim MS; The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Res Sq ; 2023 Jul 19.
Article en En | MEDLINE | ID: mdl-37503119
ABSTRACT
The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across more than 1000 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the Homo sapiens and Mus musculus genomes. All experimental data, metadata, and associated computational analyses created by the ENCODE consortium are submitted to the Data Coordination Center (DCC) for validation, tracking, storage, and distribution to community resources and the scientific community. The ENCODE project has engineered and distributed uniform processing pipelines in order to promote data provenance and reproducibility as well as allow interoperability between genomic resources and other consortia. All data files, reference genome versions, software versions, and parameters used by the pipelines are captured and available via the ENCODE Portal. The pipeline code, developed using Docker and Workflow Description Language (WDL; https//openwdl.org/) is publicly available in GitHub, with images available on Dockerhub (https//hub.docker.com), enabling access to a diverse range of biomedical researchers. ENCODE pipelines maintained and used by the DCC can be installed to run on personal computers, local HPC clusters, or in cloud computing environments via Cromwell. Access to the pipelines and data via the cloud allows small labs the ability to use the data or software without access to institutional compute clusters. Standardization of the computational methodologies for analysis and quality control leads to comparable results from different ENCODE collections - a prerequisite for successful integrative analyses.
Palabras clave
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: Res Sq Año: 2023 Tipo del documento: Article País de afiliación: Estados Unidos
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: Res Sq Año: 2023 Tipo del documento: Article País de afiliación: Estados Unidos