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9 materials found

Authors: Gary Bader  or malloryfreeberg 


Pathways and Network Analysis of -Omics data 2018 Module 3-Network Visualization and Analysis with Cytoscape

Course covers the bioinformatics concepts and tools available for interpreting a gene list using pathway and network information.

Pathways and Network Analysis of -Omics data 2018 Module 3-Network Visualization and Analysis with Cytoscape http://tess.elixir-uk.org/materials/pathways-and-network-analysis-of-omics-data-2018-module-3-network-visualization-and-analysis-with-cytoscape Course covers the bioinformatics concepts and tools available for interpreting a gene list using pathway and network information. Researchers Graduate students Post-Doctoral Fellows Biologists, Genomicists, Computer Scientists
Pathways and Network Analysis of -Omics Data 2018 Module 1-Introduction to Pathway and Network Analysis

Course covers the bioinformatics concepts and tools available for interpreting a gene list using pathway and network information.

Pathways and Network Analysis of -Omics Data 2018 Module 1-Introduction to Pathway and Network Analysis http://tess.elixir-uk.org/materials/pathways-and-network-analysis-of-omics-data-2018-module-1-introduction-to-pathway-and-network-analysis Course covers the bioinformatics concepts and tools available for interpreting a gene list using pathway and network information. Researchers Post-Doctoral Fellows Biologists, Genomicists, Computer Scientists Graduate Students
Pathways and Network Analysis of -Omics Data 2017 Module 3-Network Visualization and Analysis with Cytoscape

Course covers the bioinformatics tools available for analyzing and conducting pathway and network analysis on a gene list.

Pathways and Network Analysis of -Omics Data 2017 Module 3-Network Visualization and Analysis with Cytoscape http://tess.elixir-uk.org/materials/pathways-and-network-analysis-of-omics-data-2017-module-3-network-visualization-and-analysis-with-cytoscape Course covers the bioinformatics tools available for analyzing and conducting pathway and network analysis on a gene list.
Pathways and Network Analysis 2017 Module 2-Finding Over-Represented Pathways

Course covers the bioinformatics tools available for analyzing and conducting pathway and network analysis on a gene list.

Pathways and Network Analysis 2017 Module 2-Finding Over-Represented Pathways http://tess.elixir-uk.org/materials/pathways-and-network-analysis-2017-module-2-finding-over-represented-pathways Course covers the bioinformatics tools available for analyzing and conducting pathway and network analysis on a gene list.
Pathways and Network Analysis of -Omics Data 2017 Module 1-Introduction to Pathway and Network Analysis

Course covers the bioinformatics tools available for analyzing and conducting pathway and network analysis on a gene list.

Pathways and Network Analysis of -Omics Data 2017 Module 1-Introduction to Pathway and Network Analysis http://tess.elixir-uk.org/materials/pathways-and-network-analysis-of-omics-data-2017-module-1-introduction-to-pathway-and-network-analysis Course covers the bioinformatics tools available for analyzing and conducting pathway and network analysis on a gene list. Researchers Biologists, Genomicists, Computer Scientists Graduate Students Post-Doctoral Fellows
ChIP-Seq data analysis - Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1)

ChIP-sequencing is a method used to analyze protein interactions with DNA. Questions of the tutorial: - How is raw ChIP-seq data processed and analyzed? - What are the binding sites of Tal1? - Which genes are regulated by Tal1? Objectives of the tutorial: - Inspect read quality with FastQC -...

Resource type: Tutorial

ChIP-Seq data analysis - Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) http://tess.elixir-uk.org/materials/chip-seq-data-analysis-identification-of-the-binding-sites-of-the-t-cell-acute-lymphocytic-leukemia-protein-1-tal1 ChIP-sequencing is a method used to analyze protein interactions with DNA. Questions of the tutorial: - How is raw ChIP-seq data processed and analyzed? - What are the binding sites of Tal1? - Which genes are regulated by Tal1? Objectives of the tutorial: - Inspect read quality with FastQC - Perform read trimming with Trimmomatic - Align trimmed reads with BWA - Assess quality and reproducibility of experiments - Identify Tal1 binding sites with MACS2 - Determine unique/common Tal1 binding sites from G1E and Megakaryocytes - Identify unique/common Tal1 peaks occupying gene promoters - Visually inspect Tal1 peaks with Trackster
Transcriptomics - Reference-based RNA-Seq data analysis

Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - What are the effects of Pasilla (PS) gene depletion on splicing events? - How to analyze RNA sequencing data using a reference genome? Objectives of the tutorial: - Analysis of RNA sequencing data using...

Resource type: Tutorial

Transcriptomics - Reference-based RNA-Seq data analysis http://tess.elixir-uk.org/materials/transcriptomics-reference-based-rna-seq-data-analysis Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - What are the effects of Pasilla (PS) gene depletion on splicing events? - How to analyze RNA sequencing data using a reference genome? Objectives of the tutorial: - Analysis of RNA sequencing data using a reference genome - Analysis of differentially expressed genes - Identification of functional enrichment among differentially expressed genes
Transcriptomics - Differential abundance testing of small RNAs

Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - What small RNAs are expressed? - What RNA features have significantly different numbers of small RNAs targeting them between two conditions? Objectives of the tutorial: - Process small RNA-seq datasets...

Resource type: Tutorial

Transcriptomics - Differential abundance testing of small RNAs http://tess.elixir-uk.org/materials/transcriptomics-differential-abundance-testing-of-small-rnas Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - What small RNAs are expressed? - What RNA features have significantly different numbers of small RNAs targeting them between two conditions? Objectives of the tutorial: - Process small RNA-seq datasets to determine quality and reproducibility. - Filter out contaminants (e.g. rRNA reads) in small RNA-seq datasets. - Differentiate between subclasses of small RNAs based on their characteristics. - Identify differently abundant small RNAs and their targets.
Transcriptomics - De novo transcriptome reconstruction with RNA-Seq

Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - What genes are differentially expressed between G1E cells and megakaryocytes? - How can we generate a transcriptome de novo from RNA sequencing data? Objectives of the tutorial: - Analysis of RNA...

Resource type: Tutorial

Transcriptomics - De novo transcriptome reconstruction with RNA-Seq http://tess.elixir-uk.org/materials/transcriptomics-de-novo-transcriptome-reconstruction-with-rna-seq Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - What genes are differentially expressed between G1E cells and megakaryocytes? - How can we generate a transcriptome de novo from RNA sequencing data? Objectives of the tutorial: - Analysis of RNA sequencing data using a reference genome - Reconstruction of transcripts without reference transcriptome (de novo) - Analysis of differentially expressed genes