Register training material
1447 materials found

Analyzing Patient Data

Analyzing Patient Data from https://github.com/swcarpentry/bc/tree/gh-pages/novice/matlab/01-intro.md.

Keywords: Matlab

Analyzing Patient Data https://tess.elixir-europe.org/materials/analyzing-patient-data Analyzing Patient Data from https://github.com/swcarpentry/bc/tree/gh-pages/novice/matlab/01-intro.md. Matlab Novice
Making Choices

Making Choices from https://github.com/swcarpentry/bc/tree/gh-pages/novice/matlab/04-cond.md.

Keywords: Matlab

Making Choices https://tess.elixir-europe.org/materials/making-choices Making Choices from https://github.com/swcarpentry/bc/tree/gh-pages/novice/matlab/04-cond.md. Matlab Novice
Creating Functions

Creating Functions from https://github.com/swcarpentry/bc/tree/gh-pages/novice/matlab/03-func.md.

Keywords: Matlab

Creating Functions https://tess.elixir-europe.org/materials/creating-functions Creating Functions from https://github.com/swcarpentry/bc/tree/gh-pages/novice/matlab/03-func.md. Matlab Novice
Defensive Programming

Defensive Programming from https://github.com/swcarpentry/bc/tree/gh-pages/novice/matlab/05-defensive.md.

Keywords: Matlab

Defensive Programming https://tess.elixir-europe.org/materials/defensive-programming Defensive Programming from https://github.com/swcarpentry/bc/tree/gh-pages/novice/matlab/05-defensive.md. Matlab Novice
Collaborating

Collaborating from https://github.com/swcarpentry/bc/tree/gh-pages/novice/hg/02-collab.md.

Keywords: Hg

Collaborating https://tess.elixir-europe.org/materials/collaborating Collaborating from https://github.com/swcarpentry/bc/tree/gh-pages/novice/hg/02-collab.md. Hg Novice
A Better Kind of Backup

A Better Kind of Backup from https://github.com/swcarpentry/bc/tree/gh-pages/novice/git/01-backup.md.

Keywords: Git

A Better Kind of Backup https://tess.elixir-europe.org/materials/a-better-kind-of-backup A Better Kind of Backup from https://github.com/swcarpentry/bc/tree/gh-pages/novice/git/01-backup.md. Git Novice
Introducing Version Control

Introducing Version Control from https://github.com/swcarpentry/bc/tree/gh-pages/novice/hg/00-intro.md.

Keywords: Hg

Introducing Version Control https://tess.elixir-europe.org/materials/introducing-version-control Introducing Version Control from https://github.com/swcarpentry/bc/tree/gh-pages/novice/hg/00-intro.md. Hg Novice
Open Science

Open Science from https://github.com/swcarpentry/bc/tree/gh-pages/novice/hg/04-open.md.

Keywords: Hg

Open Science https://tess.elixir-europe.org/materials/open-science Open Science from https://github.com/swcarpentry/bc/tree/gh-pages/novice/hg/04-open.md. Hg Novice
Conflicts

Conflicts from https://github.com/swcarpentry/bc/tree/gh-pages/novice/hg/03-conflict.md.

Keywords: Hg

Conflicts https://tess.elixir-europe.org/materials/conflicts Conflicts from https://github.com/swcarpentry/bc/tree/gh-pages/novice/hg/03-conflict.md. Hg Novice
Code Review

Code Review from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/03-review.md.

Keywords: Extras

Code Review https://tess.elixir-europe.org/materials/code-review Code Review from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/03-review.md. Extras Novice
Shell Variables

Shell Variables from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/06-shellvar.md.

Keywords: Extras

Shell Variables https://tess.elixir-europe.org/materials/shell-variables Shell Variables from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/06-shellvar.md. Extras Novice
Exceptions

Exceptions from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/08-exceptions.md.

Keywords: Extras

Exceptions https://tess.elixir-europe.org/materials/exceptions Exceptions from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/08-exceptions.md. Extras Novice
Permissions

Permissions from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/01-perm.md.

Keywords: Shell

Permissions https://tess.elixir-europe.org/materials/permissions Permissions from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/01-perm.md. Shell Intermediate
Forking a Repository

Forking a Repository from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/02-forking.md.

Keywords: Extras

Forking a Repository https://tess.elixir-europe.org/materials/forking-a-repository Forking a Repository from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/02-forking.md. Extras Novice
Numbers

Numbers from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/09-numbers.md.

Keywords: Extras

Numbers https://tess.elixir-europe.org/materials/numbers Numbers from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/09-numbers.md. Extras Novice
Branching in Git

Branching in Git from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/01-branching.md.

Keywords: Extras

Branching in Git https://tess.elixir-europe.org/materials/branching-in-git Branching in Git from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/01-branching.md. Extras Novice 2013-08-22
Manual Pages

Manual Pages from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/04-man.md.

Keywords: Extras

Manual Pages https://tess.elixir-europe.org/materials/manual-pages Manual Pages from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/04-man.md. Extras Novice
Why I Teach

Why I Teach from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/10-why.md.

Keywords: Extras

Why I Teach https://tess.elixir-europe.org/materials/why-i-teach Why I Teach from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/10-why.md. Extras Novice
Working Remotely

Working Remotely from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/02-ssh.md.

Keywords: Shell

Working Remotely https://tess.elixir-europe.org/materials/working-remotely Working Remotely from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/02-ssh.md. Shell Intermediate
SCOP

Introduction to some of the features of SCOP.

SCOP https://tess.elixir-europe.org/materials/scop Introduction to some of the features of SCOP. 2017-10-05
DISOPRED, FFPred, MEMPACK

Introduction to some of the features of the DISOPRED/FFPred/MEMPACK resources.

DISOPRED, FFPred, MEMPACK https://tess.elixir-europe.org/materials/disopred-ffpred-mempack Introduction to some of the features of the DISOPRED/FFPred/MEMPACK resources. 2017-10-05
FUGUE/VIVACE

Introduction to some of the features of the FUGUE/VIVACE resources.

FUGUE/VIVACE https://tess.elixir-europe.org/materials/fugue-vivace Introduction to some of the features of the FUGUE/VIVACE resources. 2017-10-05
PHYRE2

Introduction to some of the features of PHYRE2.

PHYRE2 https://tess.elixir-europe.org/materials/phyre2 Introduction to some of the features of PHYRE2. 2017-10-05
CATH/Gene3D

Introduction to some of the features of the CATH/Gene3D resources.

CATH/Gene3D https://tess.elixir-europe.org/materials/cath-gene3d Introduction to some of the features of the CATH/Gene3D resources. 2017-10-05
SUPERFAMILY

Introduction to some of the domain assignment and phylogenetic features of the SUPERFAMILY database.

SUPERFAMILY https://tess.elixir-europe.org/materials/superfamily Introduction to some of the domain assignment and phylogenetic features of the SUPERFAMILY database. 2017-10-05
Genome3D Structures

Introduction to examining and comparing Genome3D's 3D structural models

Genome3D Structures https://tess.elixir-europe.org/materials/genome3d-structures Introduction to examining and comparing Genome3D's 3D structural models 2017-10-05
Search

Introduction to Genome3D's search abilities

Search https://tess.elixir-europe.org/materials/search Introduction to Genome3D's search abilities 2017-10-05
High-throughput sequencing training materials repository

This repository includes training materials on the analysis of high-throughput sequencing (HTS) data, on the following topics: Introduction to HTS, RNA-seq, ChIP-seq and variant calling analysis. Materials have been annotated following the standards and guidelines proposed at the “Best practices...

Scientific topics: Data architecture, analysis and design, Bioinformatics

Keywords: High throughput sequencing analysis, Rna seq chip seq anayses, Variant calling

High-throughput sequencing training materials repository https://tess.elixir-europe.org/materials/high-throughput-sequencing-training-materials-repository This repository includes training materials on the analysis of high-throughput sequencing (HTS) data, on the following topics: Introduction to HTS, RNA-seq, ChIP-seq and variant calling analysis. Materials have been annotated following the standards and guidelines proposed at the “Best practices in next-generation sequencing data analysis” workshop which took place at the University of Cambridge, UK, on 13-14 January 2015. Following this workshop, a Git repository has been set up for sharing annotated materials. This repository uses Git, hence it is decentralized and self-managed by the community and can be forked/built-upon by all users. Data architecture, analysis and design Bioinformatics High throughput sequencing analysis, Rna seq chip seq anayses, Variant calling Life Science Researchers PhD students Trainers beginner bioinformaticians post-docs 2015-12-17 2017-10-09
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
Metagenomics 2015

Link to the GitHub repo containing all the publicly available files from the 2015 Metagenomics course held at TGAC in November 2015

Scientific topics: Metagenomics

Keywords: Metagenomics

Metagenomics 2015 https://tess.elixir-europe.org/materials/metagenomics-2015 Link to the GitHub repo containing all the publicly available files from the 2015 Metagenomics course held at TGAC in November 2015 Metagenomics Metagenomics PhD post-docs 2015-11-23 2017-10-09