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1023 materials found
Transcriptomics - CLIP-Seq data analysis from pre-processing to motif detection

Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - How is raw CLIP-Seq data processed and analysed? - How do I find binding motifs and targets for a protein (e.g., RBFOX2)? Objectives of the tutorial: - Remove Adapters, Barcodes and Unique Molecular...

Resource type: Tutorial

Transcriptomics - CLIP-Seq data analysis from pre-processing to motif detection https://tess.elixir-europe.org/materials/transcriptomics-clip-seq-data-analysis-from-pre-processing-to-motif-detection Training material for all kinds of transcriptomics analysis. Questions of the tutorial: - How is raw CLIP-Seq data processed and analysed? - How do I find binding motifs and targets for a protein (e.g., RBFOX2)? Objectives of the tutorial: - Remove Adapters, Barcodes and Unique Molecular Identifiers (UMIs) from the reads - Align trimmed reads with STAR - De-duplicate the read library - Inspect the read mapping and de-duplication quality - Perform peak calling with PEAKachu - Analyse the peaks and find potential binding motifs and targets - Check the quality of the peak calling
Summer School 2018 TrainMalta: Epigenomics. Introduction to Unix and R

An overview of Unix and R for bioinformatics

Keywords: Unix, R-programming

Resource type: Training materials

Summer School 2018 TrainMalta: Epigenomics. Introduction to Unix and R https://tess.elixir-europe.org/materials/summer-school-2018-trainmalta-epigenomics-introduction-to-unix-and-r An overview of Unix and R for bioinformatics Luigi Grassi Unix, R-programming PhD students Life Science Researchers
Programming in the Life Sciences

This is a OER around a six day course on using JavaScript to program the life sciences web, but with a focus on the Open PHACTS API.

Scientific topics: Pharmacology, Drug discovery

Programming in the Life Sciences https://tess.elixir-europe.org/materials/programming-in-the-life-sciences This is a OER around a six day course on using JavaScript to program the life sciences web, but with a focus on the Open PHACTS API. Pharmacology Drug discovery bioinformaticians
High Performance Computing in Life Sciences

No description provided.

High Performance Computing in Life Sciences https://tess.elixir-europe.org/materials/high-performance-computing-in-life-sciences No description provided.
Pathway module of ArrayAnalysis.org

This tutorial explains how to use the Pathway module of ArrayAnalysis.org for pathway analysis of microarray data.

Keywords: Gene Ontology

Pathway module of ArrayAnalysis.org https://tess.elixir-europe.org/materials/pathway-module-of-arrayanalysis-org This tutorial explains how to use the Pathway module of ArrayAnalysis.org for pathway analysis of microarray data. Gene Ontology PhD students post-docs
Data Carpentry in R

Data Carpentry workshops are for any researcher who has data they want to analyze, and no prior computational experience is required. This hands-on workshop teaches basic concepts, skills and tools for working more effectively with data. We will cover Data organization in spreadsheets, data...

Keywords: Data analysis, Data carpentry, SoftwareCarpentry

Resource type: course materials

Data Carpentry in R https://tess.elixir-europe.org/materials/data-carpentry-in-r Data Carpentry workshops are for any researcher who has data they want to analyze, and no prior computational experience is required. This hands-on workshop teaches basic concepts, skills and tools for working more effectively with data. We will cover Data organization in spreadsheets, data cleaning with OpenRefine, and learn how to use the statistical program R. If time allows we will also talk about Interacting with databases from R. Participants will be encouraged to help one another and to apply what they have learned to their own research problems Data analysis, Data carpentry, SoftwareCarpentry Anyone
Data visualisation with R and ggplot2

This course provides a short beginners introduction to data visualisation using the R programming language and software environment for statistical computing and graphics. Sergio will demonstrate basic examples on how to import data, perform different types of plots and export graphics using R...

Keywords: R-programming

Resource type: course materials

Data visualisation with R and ggplot2 https://tess.elixir-europe.org/materials/data-visualisation-with-r-and-ggplot2 This course provides a short beginners introduction to data visualisation using the R programming language and software environment for statistical computing and graphics. Sergio will demonstrate basic examples on how to import data, perform different types of plots and export graphics using R standard functions and the library ggplot2. Everybody is welcome; if you would like to follow along with your laptop, please bring R and RStudio downloaded and installed before the session. R-programming PhD students Researchers
Introduction to R

This course provides a short beginners introduction to the R programming language and software environment for statistical computing and graphics. Sergio will demonstrate basic examples on how to input, explore, plot and output data in R. Everybody is welcome, if you would like to follow along...

Keywords: R-programming

Resource type: course materials

Introduction to R https://tess.elixir-europe.org/materials/introduction-to-r-327a9c78-9b0c-4133-adfc-180c02c93023 This course provides a short beginners introduction to the R programming language and software environment for statistical computing and graphics. Sergio will demonstrate basic examples on how to input, explore, plot and output data in R. Everybody is welcome, if you would like to follow along with your laptop, please bring R and RStudio downloaded and installed before the session. R-programming PhD students Researchers
Introduction to GitHub for chemists

Are you interested in learning Git and GitHub to manage your code, manuscripts or research data? This introductory workshop will be covering the following: - Background and motivation - What is Git? What is version control? What is GitHub? - How can Git and GitHub be useful for you? -...

Keywords: Git, GitHub

Resource type: course materials

Introduction to GitHub for chemists https://tess.elixir-europe.org/materials/introduction-to-github-for-chemists Are you interested in learning Git and GitHub to manage your code, manuscripts or research data? This introductory workshop will be covering the following: - Background and motivation - What is Git? What is version control? What is GitHub? - How can Git and GitHub be useful for you? - Practical session: working with Git and GitHub Clair Castle Git, GitHub Researchers PhD students Staff
Make your academic life easy with ORCID: an introduction

Many funders and publishers now require you to get an Open Researcher and Contributor ID (ORCID): an identifier that is unique to you and which comes with you wherever you go. It eliminates ambiguity about your name so you can get full credit for your work. Do you have an ORCID id? Are you sure...

Keywords: ORCID

Resource type: Tutorial

Make your academic life easy with ORCID: an introduction https://tess.elixir-europe.org/materials/make-your-academic-life-easy-with-orcid-an-introduction Many funders and publishers now require you to get an Open Researcher and Contributor ID (ORCID): an identifier that is unique to you and which comes with you wherever you go. It eliminates ambiguity about your name so you can get full credit for your work. Do you have an ORCID id? Are you sure how best to use it? Bring your own device to this practical session and register for an ORCID id, explore its features and find out more ORCID Researchers PhD students Staff
Infectious Disease Genomic Epidemiology 2018 Module 7-Data Visualization

Course providing an introduction to genomic epidemiology analysis followed by hands-on practical tutorials demonstrating the use of selected analysis tools.

Infectious Disease Genomic Epidemiology 2018 Module 7-Data Visualization https://tess.elixir-europe.org/materials/infectious-disease-genomic-epidemiology-2018-module-7-data-visualization Course providing an introduction to genomic epidemiology analysis followed by hands-on practical tutorials demonstrating the use of selected analysis tools. Researchers Post-Doctoral Fellows Graduate students Biologists, Genomicists, Computer Scientists
Infectious Disease Genomic Epidemiology 2018 Module 6-Emerging Pathogen Detection and Identification Using Metagenomics Samples

Course providing an introduction to genomic epidemiology analysis followed by hands-on practical tutorials demonstrating the use of selected analysis tools.

Infectious Disease Genomic Epidemiology 2018 Module 6-Emerging Pathogen Detection and Identification Using Metagenomics Samples https://tess.elixir-europe.org/materials/infectious-disease-genomic-epidemiology-2018-module-6-emerging-pathogen-detection-and-identification-using-metagenomics-samples Course providing an introduction to genomic epidemiology analysis followed by hands-on practical tutorials demonstrating the use of selected analysis tools. Researchers Post-Doctoral Fellows Graduate students Biologists, Genomicists, Computer Scientists
Infectious Disease Genomic Epidemiology 2018 Module 5-Phylogeographic Analysis

Course providing an introduction to genomic epidemiology analysis followed by hands-on practical tutorials demonstrating the use of selected analysis tools.

Infectious Disease Genomic Epidemiology 2018 Module 5-Phylogeographic Analysis https://tess.elixir-europe.org/materials/infectious-disease-genomic-epidemiology-2018-module-5-phylogeographic-analysis Course providing an introduction to genomic epidemiology analysis followed by hands-on practical tutorials demonstrating the use of selected analysis tools. Researchers Graduate students Biologists, Genomicists, Computer Scientists Post-Doctoral Fellows
Infectious Disease Genomic Epidemiology 2018 Module 4-Antimicrobial Resistance Genes

Course providing an introduction to genomic epidemiology analysis followed by hands-on practical tutorials demonstrating the use of selected analysis tools.

Infectious Disease Genomic Epidemiology 2018 Module 4-Antimicrobial Resistance Genes https://tess.elixir-europe.org/materials/infectious-disease-genomic-epidemiology-2018-module-4-antimicrobial-resistance-genes Course providing an introduction to genomic epidemiology analysis followed by hands-on practical tutorials demonstrating the use of selected analysis tools. Researchers Post-Doctoral Fellows Graduate students Biologists, Genomicists, Computer Scientists
Infectious Disease Genomic Epidemiology 2018 Module 3-Pathogen Genomic Analysis 2

Course providing an introduction to genomic epidemiology analysis followed by hands-on practical tutorials demonstrating the use of selected analysis tools.

Infectious Disease Genomic Epidemiology 2018 Module 3-Pathogen Genomic Analysis 2 https://tess.elixir-europe.org/materials/infectious-disease-genomic-epidemiology-2018-module-3-pathogen-genomic-analysis-2 Course providing an introduction to genomic epidemiology analysis followed by hands-on practical tutorials demonstrating the use of selected analysis tools. Researchers Post-Doctoral Fellows Graduate Students Biologists, Genomicists, Computer Scientists
Infectious Disease Genomic Epidemiology 2018 Module 2-Pathogen Genomic Analysis 1

Course providing an introduction to genomic epidemiology analysis followed by hands-on practical tutorials demonstrating the use of selected analysis tools.

Infectious Disease Genomic Epidemiology 2018 Module 2-Pathogen Genomic Analysis 1 https://tess.elixir-europe.org/materials/infectious-disease-genomic-epidemiology-2018-module-2-pathogen-genomic-analysis-1 Course providing an introduction to genomic epidemiology analysis followed by hands-on practical tutorials demonstrating the use of selected analysis tools. Researchers Post-Doctoral Fellows Graduate students Biologists, Genomicists, Computer Scientists
Infectious Disease Genomic Epidemiology 2018 Module 1-Introduction to Public Health Microbiology and Genomic Epidemiology

Course providing an introduction to genomic epidemiology analysis followed by hands-on practical tutorials demonstrating the use of selected analysis tools.

Infectious Disease Genomic Epidemiology 2018 Module 1-Introduction to Public Health Microbiology and Genomic Epidemiology https://tess.elixir-europe.org/materials/infectious-disease-genomic-epidemiology-2018-module-1-introduction-to-public-health-microbiology-and-genomic-epidemiology Course providing an introduction to genomic epidemiology analysis followed by hands-on practical tutorials demonstrating the use of selected analysis tools. Researchers Post-Doctoral Fellows Graduate students Biologists, Genomicists, Computer Scientists
Pathways and Network Analysis of -Omics data 2018 Module 6-Regulatory 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 6-Regulatory Network Analysis https://tess.elixir-europe.org/materials/pathways-and-network-analysis-of-omics-data-2018-module-6-regulatory-network-analysis Course covers the bioinformatics concepts and tools available for interpreting a gene list using pathway and network information. Researchers Post-Doctoral Fellows Graduate students Biologists, Genomicists, Computer Scientists
Pathways and Network Analysis of -Omics data 2018 Module 5-Gene Function Prediction

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 5-Gene Function Prediction https://tess.elixir-europe.org/materials/pathways-and-network-analysis-of-omics-data-2018-module-5-gene-function-prediction Course covers the bioinformatics concepts and tools available for interpreting a gene list using pathway and network information. Researchers Post-Doctoral Fellows Graduate students Biologists, Genomicists, Computer Scientists
Pathways and Network Analysis of -Omics data 2018 Module 4-More Depth on Network and Pathway 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 4-More Depth on Network and Pathway Analysis https://tess.elixir-europe.org/materials/pathways-and-network-analysis-of-omics-data-2018-module-4-more-depth-on-network-and-pathway-analysis Course covers the bioinformatics concepts and tools available for interpreting a gene list using pathway and network information. Researchers Post-Doctoral Fellows Graduate Students Biologists, Genomicists, Computer Scientists
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 https://tess.elixir-europe.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 2-Finding Over-Represented Pathways

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 2-Finding Over-Represented Pathways https://tess.elixir-europe.org/materials/pathways-and-network-analysis-of-omics-data-2018-module-2-finding-over-represented-pathways 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 https://tess.elixir-europe.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
Epigenomic Data Analysis 2018 Module 4-Downstream Analyses and Integrative Tools

Course providing an introduction to histone ChiP-Seq and WGBS data analysis followed by integrated tutorials demonstrating the use of open source ChiP-Seq and WGBS analysis packages.

Epigenomic Data Analysis 2018 Module 4-Downstream Analyses and Integrative Tools https://tess.elixir-europe.org/materials/epigenomic-data-analysis-2018-module-4-downstream-analyses-and-integrative-tools Course providing an introduction to histone ChiP-Seq and WGBS data analysis followed by integrated tutorials demonstrating the use of open source ChiP-Seq and WGBS analysis packages. Researchers Post-Doctoral Fellows Biologists, Genomicists, Computer Scientists Graduate Students
Epigenomic Data Analysis 2018 Module 3-Introduction to WGBS and Analysis

Course providing an introduction to histone ChiP-Seq and WGBS data analysis followed by integrated tutorials demonstrating the use of open source ChiP-Seq and WGBS analysis packages.

Epigenomic Data Analysis 2018 Module 3-Introduction to WGBS and Analysis https://tess.elixir-europe.org/materials/epigenomic-data-analysis-2018-module-3-introduction-to-wgbs-and-analysis Course providing an introduction to histone ChiP-Seq and WGBS data analysis followed by integrated tutorials demonstrating the use of open source ChiP-Seq and WGBS analysis packages. Researchers Post-Doctoral Fellows Biologists, Genomicists, Computer Scientists Graduate Students
Epigenomic Data Analysis 2018 Module 2-ChIP-Seq Alignment, Peak Calling, and Visualization

Course providing an introduction to histone ChiP-Seq and WGBS data analysis followed by integrated tutorials demonstrating the use of open source ChiP-Seq and WGBS analysis packages.

Epigenomic Data Analysis 2018 Module 2-ChIP-Seq Alignment, Peak Calling, and Visualization https://tess.elixir-europe.org/materials/epigenomic-data-analysis-2018-module-2-chip-seq-alignment-peak-calling-and-visualization Course providing an introduction to histone ChiP-Seq and WGBS data analysis followed by integrated tutorials demonstrating the use of open source ChiP-Seq and WGBS analysis packages. Researchers Graduate students Post-Doctoral Fellows Biologists, Genomicists, Computer Scientists
Epigenomic Data Analysis 2018 Module 1-Introduction to ChIP Sequencing and Analysis

Course providing an introduction to histone ChiP-Seq and WGBS data analysis followed by integrated tutorials demonstrating the use of open source ChiP-Seq and WGBS analysis packages.

Epigenomic Data Analysis 2018 Module 1-Introduction to ChIP Sequencing and Analysis https://tess.elixir-europe.org/materials/epigenomic-data-analysis-2018-module-1-introduction-to-chip-sequencing-and-analysis Course providing an introduction to histone ChiP-Seq and WGBS data analysis followed by integrated tutorials demonstrating the use of open source ChiP-Seq and WGBS analysis packages. Researchers Post-Doctoral Fellows Graduate Students Biologists, Genomicists, Computer Scientists
Bioinformatics of Genomic Medicine 2018 Module 7-Identifying Integrative Subtypes and Building Classifiers

Course will explore various aspects of genomic medicine, covering and teaching popular tools and methods in the field.

Bioinformatics of Genomic Medicine 2018 Module 7-Identifying Integrative Subtypes and Building Classifiers https://tess.elixir-europe.org/materials/bioinformatics-of-genomic-medicine-2018-module-7-identifying-integrative-subtypes-and-building-classifiers Course will explore various aspects of genomic medicine, covering and teaching popular tools and methods in the field. Researchers Post-Doctoral Fellows Graduate students Biologists, Genomicists, Computer Scientists
Bioinformatics of Genomic Medicine 2018 Module 6-Epigenetic Profiling in Disease

Course will explore various aspects of genomic medicine, covering and teaching popular tools and methods in the field.

Bioinformatics of Genomic Medicine 2018 Module 6-Epigenetic Profiling in Disease https://tess.elixir-europe.org/materials/bioinformatics-of-genomic-medicine-2018-module-6-epigenetic-profiling-in-disease Course will explore various aspects of genomic medicine, covering and teaching popular tools and methods in the field. Researchers Post-Doctoral Fellows Graduate Students Biologists, Genomicists, Computer Scientists
Bioinformatics of Genomic Medicine 2018 Module 5-Available Epigenetics Data and Resources

Course will explore various aspects of genomic medicine, covering and teaching popular tools and methods in the field.

Bioinformatics of Genomic Medicine 2018 Module 5-Available Epigenetics Data and Resources https://tess.elixir-europe.org/materials/bioinformatics-of-genomic-medicine-2018-module-5-available-epigenetics-data-and-resources Course will explore various aspects of genomic medicine, covering and teaching popular tools and methods in the field. Researchers Post-Doctoral Fellows Graduate students Biologists, Genomicists, Computer Scientists