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Keywords: RNA-Seq 


ADER19F - Analysis of Differential Expression with RNAseq (First course in 2019)

This introductory course covers practical aspects of the analysis of differential gene expression by RNAseq, from planning the gathering of sequence data to the generation of tables of differentially expressed gene lists and visualization of results. For this edition of the course, we will also...

Keywords: RNA-Seq, Genomics, RNA

Resource type: Documentation, Exercise, Handout, Scripts

ADER18S - Analysis of Differential Expression with RNAseq (Second course in 2018)

This introductory course covers practical aspects of the analysis of differential gene expression by RNAseq, from planning the gathering of sequence data to the generation of tables of differentially expressed gene lists and visualization of results. For this edition of the course, we will also...

Keywords: RNA-Seq, Genomics, RNA

Resource type: Documentation, Exercise, Handout, Scripts

ADER18F - Analysis of Differential Expression with RNAseq (First course in 2018)

This introductory course covers practical aspects of the analysis of differential gene expression by RNAseq, from planning the gathering of sequence data to the generation of tables of differentially expressed gene lists and visualization of results. We we will also cover some of the initial...

Keywords: RNA-Seq, Genomics, RNA

Resource type: Documentation, Exercise, Handout, Scripts

Single cell RNA-seq data analysis with R

Programme

Monday 27.5.2019

Introduction to single cell RNA-seq (Jules Gilet)
Quality control and data preprocessing (Åsa Björklund)
Normalisation (Heli Pessa)
Removal of confounding factors (Bishwa Ghimire)
Data integration (CCA, MNN, dataset alignment) (Ahmed Mahfouz)

Tuesday...

Scientific topics: RNA-Seq

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

Resource type: course materials

RNA-seq data analysis using Chipster

Materials from the ELIXIR tutorial “RNA-seq data analysis using Chipster”, Jan 31, 2017

Scientific topics: Genomics, Transcriptomics

Keywords: transcriptomics, RNA-Seq, eLearning, EeLP

Resource type: course materials, Training materials, Slides, Video

Single cell RNA-seq data analysis with R

This hands-on course introduces the participants to single cell RNA-seq data analysis concepts and popular R packages. It covers the preprocessing steps from raw sequence reads to expression matrix as well as clustering, cell type identification, differential expression analysis and pseudotime...

Scientific topics: RNA-Seq

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

Resource type: course materials

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

LXDE RStudio with support for bioconductor tools

An LXDE Rstudio with pre-loaded Bioconductor tools for rna-seq DE analysis & visualisation

Keywords: RNA-Seq, IFR, Institute of Food Research, Quadram Institute

IFR Dockerised version of the EBI's Introduction to RNA-seq course

This is basically the EBI RNA-seq course bundled up in a Docker container using LXDE via TightVNC to provide a graphical environment. The material has been repackaged to use an Ipython Notebook as the learning environment which can be annotated by the learner.

Keywords: RNA-Seq, IFR, Institute of Food Research, Quadram Institute