Authors: Manuel Corpas or Eija Korpelainen
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
Materials from the asynchronous learning course "ELIXIR eLearning definitions"
Keywords: eLearning, training, EeLP
Resource type: course materials, Training materials, Documentation
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
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
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
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
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 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
Introduction to BioJS a standard for visualisation of biological data in JavaScript
Keywords: Biojs, Javascript, Software, Standards
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
Presention
Keywords: Goblet
This is a presentation I gave at the Jornadas de Bioinformática in Seville, Spain (24/09/14)
Keywords: Goblet, Training portal
I present the points of view, the challenges and advantages of developing training materials through the cloud.
Keywords: Advanced bioinformatics training, Cloud computing, Training
I give an overview of the analysis of gene expression in plants using RNA-seq data. This course provides a foundation on the tuxedo software suite: TopHat, Cufflinks, CummeRbund.