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
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
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
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
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 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
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
An LXDE Rstudio with pre-loaded Bioconductor tools for rna-seq DE analysis & visualisation
Keywords: RNA-Seq, IFR, Institute of Food Research, Quadram Institute
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
Working Remotely from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/07-ssh.md.
Keywords: Extras
Keywords: Extras
Keywords: Extras
Shell Variables from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/06-shellvar.md.
Keywords: Extras
Keywords: Extras
Forking a Repository from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/02-forking.md.
Keywords: Extras
Keywords: Extras
Branching in Git from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/01-branching.md.
Keywords: Extras
Manual Pages from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/04-man.md.
Keywords: Extras
Why I Teach from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/10-why.md.
Keywords: Extras