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2 materials found

Content provider: GOBLET 

and

Authors: Jared Simpson  or Eija Korpelainen  or Maria Victoria .  or Julie Sullivan  or Friederike Ehrhart  or nekrut  or Boris Steipe  or Monica Munoz-Torres 


BD2K Data Science Open Educational Resources (OERs)

These Online Educational Resources (OERs) cover a variety of topics related to data science and are intended for use in courses, programs, workshops, and related activities. Modules relevant to biocuration:BDK05 Basic Research Data Standards...

Scientific topics: Ontology

Keywords: Biocuration, Curation, Identifiers, Ontology, Standards

BD2K Data Science Open Educational Resources (OERs) https://tess.elixir-europe.org/materials/bd2k-data-science-open-educational-resources-oers These Online Educational Resources (OERs) cover a variety of topics related to data science and are intended for use in courses, programs, workshops, and related activities. Modules relevant to biocuration:BDK05 Basic Research Data Standards (https://github.com/OHSUBD2K/BDK05-Basic-Research-Data-Standards). Standards for biomedical data, participating in communities that develop them, aiding reproducibility.BDK11 Identifiers (https://github.com/OHSUBD2K/BDK11-Identifiers). Introduction to identifiers (modeling, identifying and describing resources and objects.)BDK12 Data Annotation And Curation (https://github.com/OHSUBD2K/BDK12-Data-annotation-and-curation). Data preparation, developing standardized quality assurance processes and pipelines.BDK14 Ontologies 101 (https://github.com/OHSUBD2K/BDK14-Ontologies-101). Introduction to OWL2 and data reasoning.Authors: OHSU BD2K teamType of Material: Presentation slides, videos (in BDK12), exercises, and other resources.License: CC-BY Ontology Biocuration, Curation, Identifiers, Ontology, Standards biocurators 2018-04-02
RNA-seq data analysis: from raw reads to differentially expressed genes

This course material introduces the central concepts, analysis steps and file formats in RNA-seq data analysis. It covers the analysis from quality control to differential expression detection, and workflow construction and several data visualizations are also practised. The material consists of...

Scientific topics: Sequencing, RNA, Data architecture, analysis and design, Bioinformatics

Keywords: Bioinformatics, Differential expression, Ngs, Rna seq

RNA-seq data analysis: from raw reads to differentially expressed genes https://tess.elixir-europe.org/materials/rna-seq-data-analysis-from-raw-reads-to-differentially-expressed-genes This course material introduces the central concepts, analysis steps and file formats in RNA-seq data analysis. It covers the analysis from quality control to differential expression detection, and workflow construction and several data visualizations are also practised. The material consists of 10-30 minute lectures intertwined with hands-on exercises, and it can be accomplished in a day. As the user-friendly Chipster software is used in the exercises, no prior knowledge of R/Bioconductor or Unix ir required, and the course is thus suitable for everybody. Our book RNA-seq data analysis: A practical approach (CRC Press) can be used as background reading. The following topics and analysis tools are covered: 1. Introduction to the Chipster analysis platform 2. Quality control of raw reads (FastQC, PRINSEQ) 3. Preprocessing (Trimmomatic, PRINSEQ) 4. Alignment to reference genome (TopHat2) 5. Alignment level quality control (RseQC) 6. Quantitation (HTSeq) 7. Experiment level quality control with PCA and MDS plots 8. Differential expression analysis (DESeq2, edgeR) -normalization -dispersion estimation -statistical testing -controlling for batch effects, multifactor designs -filtering -multiple testing correction 9. Visualization of reads and results -genome browser -Venn diagram -volcano plot -plotting normalized counts for a gene -expression profiles 10. Experimental design Sequencing RNA Data architecture, analysis and design Bioinformatics Bioinformatics, Differential expression, Ngs, Rna seq Bench biologists Life Science Researchers 2015-12-04 2017-10-09