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14 materials found

Authors: erasche  or Eija Korpelainen 


Single cell RNA-seq data analysis using Chipster

This course introduces single cell RNA-seq data analysis methods, tools and file formats. 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...

Keywords: scRNA-seq

Resource type: Slides, Training materials

ELIXIR eLearning definitions

Materials from the asynchronous learning course "ELIXIR eLearning definitions"

Keywords: eLearning, training, EeLP

Resource type: course materials, Training materials, Documentation

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

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...

Scientific topics: RNA-Seq

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

Resource type: course materials, Video

Galaxy Server administration - Ansible

Resources related to configuration and maintenance of Galaxy servers

Questions of the tutorial:

  • Why Ansible?
  • How and when to use Ansible?
  • How to write a role?
  • How to leverage community build roles?

Objectives of the tutorial:

  • Learn Ansible basics
  • Write a simple role
  • Install a...

Resource type: Tutorial

Data Manipulation - Collections: Rule Based Uploader

A collection of microtutorials explaining data manipulation within Galaxy

Questions of the tutorial:

  • How to use the rule based uploader to create complex collections

Objectives of the tutorial:

  • Learn about the Rule Based Uploader

Resource type: Tutorial

Contributing to the Galaxy Training Material - Creating a new tutorial - Slides

Galaxy is a great solution to train the bioinformatics concepts: numerous bioinformatics tools are available (almost 5,000 in the ToolShed), it can be used by people without amy computer science skills, it trains to use technology, outlining available resources and efforts that have made them...

Resource type: Slides

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

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

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

Metagenomics data analysis

Metagenomics investigates the composition and function of microbial communities in different environments based on direct isolation of genetic material. It has been accelerated by the advances in high-throughput sequencing technologies, and the increasing data sizes require efficient analysis...

Scientific topics: Metagenomics

Resource type: Video, course materials

Development in Galaxy - Galaxy Interactive Environments

Galaxy is an open-source project. Everyone can contribute to its development with core Galaxy development, integration of softwares in Galaxy environment, ...

Questions of the tutorial:

  • What are Galaxy Interactive Environments (GIEs)?
  • How to enable GIEs in Galaxy?
  • How to develop your own...

Resource type: Slides

Galaxy Server administration - Advanced customisation of a Galaxy instance

Resources related to configuration and maintenance of Galaxy servers

Resource type: Slides

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