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Target audience: Training Designers  or Life Science Researchers 

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Authors: Eija Korpelainen  or Maria Victoria .  or Julie Sullivan  or Friederike Ehrhart  or Michael Love 

Rare Disease Pathway and Network Analysis

The European Joint Project on Rare Diseases (EJP-RD) and the Helis Academy organized a workshop with training for pathway and network analysis.

Keywords: Pathway analysis, Biological networks, Network analysis, Pathways

Resource type: Tutorial

Rare Disease Pathway and Network Analysis https://tess.elixir-europe.org/materials/rare-disease-pathway-and-network-analysis The European Joint Project on Rare Diseases (EJP-RD) and the Helis Academy organized a workshop with training for pathway and network analysis. Pathway analysis, Biological networks, Network analysis, Pathways Life Science Researchers
InterMine user tutorial

A tutorial for end users of InterMine

Keywords: Data querying, Data analysis, Data download, FAIR

Resource type: Tutorial

InterMine user tutorial https://tess.elixir-europe.org/materials/intermine-user-tutorial A tutorial for end users of InterMine Data querying, Data analysis, Data download, FAIR Life Science Researchers Bioinformaticians
InterMine user manual

Documentation for end users on how to search for data, run simple and complex queries, analyse results and download data from any instance of InterMine.

Keywords: Data querying, data visualization, Data download, FAIR

Resource type: Documentation

InterMine user manual https://tess.elixir-europe.org/materials/intermine-user-manual Documentation for end users on how to search for data, run simple and complex queries, analyse results and download data from any instance of InterMine. Data querying, data visualization, Data download, FAIR Life Science Researchers Bioinformaticians
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