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12 materials found

Authors: Eija Korpelainen  or Jüri Reimand 


Single cell RNA-seq data analysis using Chipster

This course introduces single cell RNA-seq data analysis. It covers the processing of transcript counts from quality control and filtering to dimensional reduction, clustering, and differential expression analysis. You will also learn how to do integrated analysis of two samples. We use Seurat v3...

Keywords: scRNA-seq

Resource type: Slides, Training materials

Single cell RNA-seq data analysis using Chipster https://tess.elixir-europe.org/materials/single-cell-rna-seq-data-analysis-using-chipster This course introduces single cell RNA-seq data analysis. It covers the processing of transcript counts from quality control and filtering to dimensional reduction, clustering, and differential expression analysis. You will also learn how to do integrated analysis of two samples. We use Seurat v3 tools embedded in the user-friendly Chipster software. scRNA-seq Biologists bioinformaticians
ELIXIR eLearning definitions

Materials from the asynchronous learning course "ELIXIR eLearning definitions"

Keywords: eLearning, training, EeLP

Resource type: course materials, Training materials, Documentation

ELIXIR eLearning definitions https://tess.elixir-europe.org/materials/elixir-elearning-definitions Materials from the asynchronous learning course "ELIXIR eLearning definitions" Brane Leskosek Jure Dimec Eija Korpelainen Teresa Attwood Sarah Morgan Nicola Mulder Celia van Gelder Patricia Palagi eLearning, training, EeLP Researchers teachers Trainers
RNA-seq data analysis using Chipster

Materials from the ELIXIR tutorial “RNA-seq data analysis using Chipster”, Jan 31, 2017

Scientific topics: Transcriptomics, Genomics

Keywords: transcriptomics, RNA-Seq, eLearning, EeLP

Resource type: course materials, Training materials, Slides, Video

RNA-seq data analysis using Chipster https://tess.elixir-europe.org/materials/rna-seq-data-analysis-using-chipster Materials from the ELIXIR tutorial “RNA-seq data analysis using Chipster”, Jan 31, 2017 Eija Korpelainen Maria Lehtivaara Transcriptomics Genomics transcriptomics, RNA-Seq, eLearning, EeLP Researchers
Single cell RNA-seq data analysis with Chipster

This course introduces single cell RNA-seq data analysis methods, tools and file formats. It covers the preprocessing steps of DropSeq data from raw reads to a digital gene expression matrix (DGE), and how to find sub-populations of cells using clustering with the Seurat tools. You will also...

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Single Cell technologies, scRNA-seq

Resource type: course materials, Video

Single cell RNA-seq data analysis with Chipster https://tess.elixir-europe.org/materials/single-cell-rna-seq-data-analysis-with-chipster-6cc8f0fb-1c92-444b-ab19-b04fe6454430 This course introduces single cell RNA-seq data analysis methods, tools and file formats. It covers the preprocessing steps of DropSeq data from raw reads to a digital gene expression matrix (DGE), and how to find sub-populations of cells using clustering with the Seurat tools. You will also learn how to compare two samples and detect conserved cluster markers and differentially expressed genes in them. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody. Eija Korpelainen RNA-Seq RNA-Seq, Single Cell technologies, scRNA-seq Biologists bioinformaticians
Bioinformatics for Cancer Genomics 2018 Module 13-Genes to Pathways

Course covers the key bioinformatics concepts and tools required to analyze cancer genomic data sets and access and work with data sets in the cloud.

Bioinformatics for Cancer Genomics 2018 Module 13-Genes to Pathways https://tess.elixir-europe.org/materials/bioinformatics-for-cancer-genomics-2018-module-13-genes-to-pathways Course covers the key bioinformatics concepts and tools required to analyze cancer genomic data sets and access and work with data sets in the cloud. Researchers Post-Doctoral Fellows Biologists, Genomicists, Computer Scientists Graduate Students
High-Throughput Biology 2017 Module 13-Finding Over-Represented Pathways

Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome.

High-Throughput Biology 2017 Module 13-Finding Over-Represented Pathways https://tess.elixir-europe.org/materials/high-throughput-biology-2017-module-13-finding-over-represented-pathways Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome. Graduate Students Researchers Biologists, Genomicists, Computer Scientists Post-Doctoral Fellows
High-Throughput Biology 2017 Module 12-Introduction to Pathway and Network Analysis

Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome.

High-Throughput Biology 2017 Module 12-Introduction to Pathway and Network Analysis https://tess.elixir-europe.org/materials/high-throughput-biology-2017-module-12-introduction-to-pathway-and-network-analysis Course covers the key bioinformatics concepts and tools required to analyze DNA- and RNA- sequence reads using a reference genome. Graduate students Researchers Post-Doctoral Fellows Biologists, Genomicists, Computer Scientists
Community analysis of amplicon sequencing data (16S rRNA)

This course introduces community analysis of amplicon sequencing data (16S rRNA). It covers preprocessing, taxonomic classification, and statistical analysis for marker gene studies. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the...

Resource type: course materials, Video

Community analysis of amplicon sequencing data (16S rRNA) https://tess.elixir-europe.org/materials/community-analysis-of-amplicon-sequencing-data-16s-rrna This course introduces community analysis of amplicon sequencing data (16S rRNA). It covers preprocessing, taxonomic classification, and statistical analysis for marker gene studies. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody.
Virus detection using small RNA-seq

This course introduces the VirusDetect pipeline covering all the analysis steps and file formats. VirusDetect allows you to detect known viruses and identify news ones by sequencing small RNAs (siRNA) in host samples. siRNA sequences are assembled to contigs and compared to known virus sequences....

Scientific topics: RNA-Seq

Resource type: course materials, Video

Virus detection using small RNA-seq https://tess.elixir-europe.org/materials/virus-detection-using-small-rna-seq This course introduces the VirusDetect pipeline covering all the analysis steps and file formats. VirusDetect allows you to detect known viruses and identify news ones by sequencing small RNAs (siRNA) in host samples. siRNA sequences are assembled to contigs and compared to known virus sequences. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody. Eija Korpelainen RNA-Seq
RNA-seq data analysis

This course introduces RNA-seq data analysis methods, tools and file formats. It covers all the steps from quality control and alignment to quantification and differential expression analysis, and also experimental design is discussed. The user-friendly Chipster software is used in the exercises,...

Scientific topics: RNA-Seq

Resource type: course materials, Video

RNA-seq data analysis https://tess.elixir-europe.org/materials/rna-seq-data-analysis-with-chipster This course introduces RNA-seq data analysis methods, tools and file formats. It covers all the steps from quality control and alignment to quantification and differential expression analysis, and also experimental design is discussed. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody. Eija Korpelainen RNA-Seq
Metagenomics data analysis

This course covers metagenomics analysis from quality control, filtering and assembly to taxonomic classification, functional assignment and comparative metagenomics. In addition to covering the analysis of whole genome shotgun sequencing data, the course has also module on community analysis of...

Scientific topics: Metagenomics

Resource type: Video, course materials

Metagenomics data analysis https://tess.elixir-europe.org/materials/metagenomics-data-analysis This course covers metagenomics analysis from quality control, filtering and assembly to taxonomic classification, functional assignment and comparative metagenomics. In addition to covering the analysis of whole genome shotgun sequencing data, the course has also module on community analysis of amplicon sequencing data (16S rRNA). Finally, international databases and standards for storing the data are introduced. The course material includes slides, exercises and lecture videos. The workshop is organized in collaboration with the ELIXIR EXCELERATE project and PRACE, and it is part of the PRACE Advanced Training Centre activity. Eija Korpelainen Metagenomics
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