Register training material
10 materials found

Target audience: Graduate Students 

and

Authors: Jared Simpson  or Michelle Brazas 


Informatics on High-Throughput Sequencing Data 2017 Module 6-De Novo Assembly

Course covers the bioinformatics tools available for managing and interpreting high-throughput sequencing data with a focus on Illumina reads.

Informatics on High-Throughput Sequencing Data 2017 Module 6-De Novo Assembly https://tess.elixir-europe.org/materials/informatics-on-high-throughput-sequencing-data-2017-module-6-de-novo-assembly Course covers the bioinformatics tools available for managing and interpreting high-throughput sequencing data with a focus on Illumina reads. Researchers Graduate Students Post-Doctoral Fellows Biologists, Genomicists, Computer Scientists
RNA-seq Analysis 2014 Module 4 - Isoform discovery and alternative expression

Explore use of Cufflinks in reference annotation based transcript (RABT) assembly mode and ‘de novo’ assembly mode. Both modes require a reference genome sequence.  

Scientific topics: RNA

Keywords: Alternative expression, Transcript isoforms

RNA-seq Analysis 2014 Module 4 - Isoform discovery and alternative expression https://tess.elixir-europe.org/materials/rna-seq-analysis-2014-module-4-isoform-discovery-and-alternative-expression Explore use of Cufflinks in reference annotation based transcript (RABT) assembly mode and ‘de novo’ assembly mode. Both modes require a reference genome sequence.   RNA Alternative expression, Transcript isoforms Biologists, Genomicists, Computer Scientists Graduate Students Post-Doctoral Fellows Researchers 2014-06-27 2017-10-09
RNA-seq Analysis 2014 Module 3 - Expression and Differential Expression

Get FPKM style expression estimates using Cufflinks Perform differential expression analysis with Cuffdiff Perform summary analysis with CummeRbund Downstream interpretation of expression analysis (multiple testing, clustering, heatmaps, classification, pathway analysis, etc.)  

Keywords: Differential expression, Transript expression

RNA-seq Analysis 2014 Module 3 - Expression and Differential Expression https://tess.elixir-europe.org/materials/rna-seq-analysis-2014-module-3-expression-and-differential-expression Get FPKM style expression estimates using Cufflinks Perform differential expression analysis with Cuffdiff Perform summary analysis with CummeRbund Downstream interpretation of expression analysis (multiple testing, clustering, heatmaps, classification, pathway analysis, etc.)   Differential expression, Transript expression Biologists, Genomicists, Computer Scientists Graduate Students Post-Doctoral Fellows Researchers 2014-06-27 2017-10-09
RNA-seq Analysis 2014 Module 2 - Alignment and Visualization

Use of Bowtie/TopHat ‘Regular mode’ vs. ‘Fusion mode’ Introduction to the BAM format Basic manipulation of BAMs with samtools, etc. Visualization of RNA-seq alignments - IGV BAM read counting and determination of variant allele expression status    

Keywords: Data visualization, Rna seq alignment

RNA-seq Analysis 2014 Module 2 - Alignment and Visualization https://tess.elixir-europe.org/materials/rna-seq-analysis-2014-module-2-alignment-and-visualization Use of Bowtie/TopHat ‘Regular mode’ vs. ‘Fusion mode’ Introduction to the BAM format Basic manipulation of BAMs with samtools, etc. Visualization of RNA-seq alignments - IGV BAM read counting and determination of variant allele expression status     Data visualization, Rna seq alignment Biologists, Genomicists, Computer Scientists Graduate Students Post-Doctoral Fellows Researchers 2014-06-27 2017-10-09
RNA-seq Analysis 2014 Module 1 - Introduction to RNA-seq Analysis

Basic introduction to biology of RNA-seq Experimental design considerations Commonly asked questions Data visualization using IGV  

Keywords: Experimental design rna seq, Igv, Introduction rna seq analysis

RNA-seq Analysis 2014 Module 1 - Introduction to RNA-seq Analysis https://tess.elixir-europe.org/materials/rna-seq-analysis-2014-module-1-introduction-to-rna-seq-analysis Basic introduction to biology of RNA-seq Experimental design considerations Commonly asked questions Data visualization using IGV   Experimental design rna seq, Igv, Introduction rna seq analysis Biologists, Genomicists, Computer Scientists Graduate Students Post-Doctoral Fellows Researchers 2014-06-27 2017-10-09
Pathway and Network Analysis 2014 Module 5 - Network Visualization

Introduction to network visualization Visualizing omics data on a network or pathway Active modules in Cytoscape

Keywords: Cytoscape, Network visualization

Pathway and Network Analysis 2014 Module 5 - Network Visualization https://tess.elixir-europe.org/materials/pathway-and-network-analysis-2014-module-5-network-visualization Introduction to network visualization Visualizing omics data on a network or pathway Active modules in Cytoscape Cytoscape, Network visualization Biologists, Genomicists, Computer Scientists Graduate Students Post-Doctoral Fellows Researchers 2014-06-26 2017-10-09
Pathway and Network Analysis 2014 Module 4 - Pathway and Network Analysis

Introduction to pathway and network analysis Basic network concepts Types of pathway and network information Pathway Databases: Reactome, KEGG, etc. Pathway analysis of large scale genomics data sets, including cancer genomics

Keywords: Biological networks, Kegg, Pathway analysis, Reactome

Pathway and Network Analysis 2014 Module 4 - Pathway and Network Analysis https://tess.elixir-europe.org/materials/pathway-and-network-analysis-2014-module-4-pathway-and-network-analysis Introduction to pathway and network analysis Basic network concepts Types of pathway and network information Pathway Databases: Reactome, KEGG, etc. Pathway analysis of large scale genomics data sets, including cancer genomics Biological networks, Kegg, Pathway analysis, Reactome Biologists, Genomicists, Computer Scientists Graduate Students Post-Doctoral Fellows Researchers 2014-06-26 2017-10-09
Pathway and Network Analysis 2014 Module 3 - Gene Regulation Analysis

Overview of transcription Data sources for regulatory data - Chromatin IP, DNA hypersensitivity, other chip data Basics of processing data Pattern discovery

Keywords: Pattern discovery, Transcriptional regulation

Pathway and Network Analysis 2014 Module 3 - Gene Regulation Analysis https://tess.elixir-europe.org/materials/pathway-and-network-analysis-2014-module-3-gene-regulation-analysis Overview of transcription Data sources for regulatory data - Chromatin IP, DNA hypersensitivity, other chip data Basics of processing data Pattern discovery Pattern discovery, Transcriptional regulation Biologists, Genomicists, Computer Scientists Graduate Students Post-Doctoral Fellows Researchers 2014-06-26 2017-10-09
Pathway and Network Analysis 2014 Module 2 - Finding Over-represented Pathways

Over-representation analysis (ORA) Statistics for detecting over-representation e.g. hypergeometric test, GSEA Multiple testing correction: Bonferroni, Benjamini-Hochberg FDR Filtering Gene Ontology e.g. using evidence codes

Keywords: Gsea, Over representation analysis

Pathway and Network Analysis 2014 Module 2 - Finding Over-represented Pathways https://tess.elixir-europe.org/materials/pathway-and-network-analysis-2014-module-2-finding-over-represented-pathways Over-representation analysis (ORA) Statistics for detecting over-representation e.g. hypergeometric test, GSEA Multiple testing correction: Bonferroni, Benjamini-Hochberg FDR Filtering Gene Ontology e.g. using evidence codes Gsea, Over representation analysis Biologists, Genomicists, Computer Scientists Graduate Students Post-Doctoral Fellows Researchers 2014-06-26 2017-10-09
Pathway and Network Analysis 2014 Module 1 - Introduction to Gene Lists

Gene list analysis overview: Workflow of concepts and tools from gene list to pathway analysis Where do gene lists come from? Working with gene function information

Keywords: Gene lists, Gene ontology

Pathway and Network Analysis 2014 Module 1 - Introduction to Gene Lists https://tess.elixir-europe.org/materials/pathway-and-network-analysis-2014-module-1-introduction-to-gene-lists Gene list analysis overview: Workflow of concepts and tools from gene list to pathway analysis Where do gene lists come from? Working with gene function information Gene lists, Gene ontology Biologists, Genomicists, Computer Scientists Graduate Students Post-Doctoral Fellows Researchers 2014-06-26 2017-10-09