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Contributors: Michael Ball  or Eija Korpelainen  or Dr. Simon Andrews  or Mr. William Edward Hill 


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 tools and 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...

Scientific topics: RNA-Seq

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

Resource type: course materials

Single cell RNA-seq data analysis with R https://tess.elixir-europe.org/materials/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 tools and 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 analysis. Eija Korpelainen RNA-Seq RNA-Seq, Single Cell technologies, scRNA-seq bioinformaticians Biologists
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 Seurat tools. You will also...

Scientific topics: RNA-Seq

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

Resource type: course materials, Video

Single cell RNA-seq data analysis with Chipster https://tess.elixir-europe.org/materials/single-cell-rna-seq-data-analysis-with-chipster-6cc8f0fb-1c92-444b-ab19-b04fe6454430 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 Seurat tools. You will also learn how to compare two samples and detect conserved cluster markers and differentially expressed genes in them. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody. Eija Korpelainen RNA-Seq RNA-Seq, Single Cell technologies, scRNA-seq Biologists bioinformaticians
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

Virus detection using small RNA-seq https://tess.elixir-europe.org/materials/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. The user-friendly Chipster software is used in the exercises, so no Unix or R experience is required and the course is thus suitable for everybody. Eija Korpelainen RNA-Seq
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

RNA-seq data analysis https://tess.elixir-europe.org/materials/rna-seq-data-analysis-with-chipster 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, so no Unix or R experience is required and the course is thus suitable for everybody. Eija Korpelainen RNA-Seq
Metagenomics data analysis

This course covers metagenomics analysis from quality control, filtering and assembly to taxonomic classification, functional assignment and comparative metagenomics. In addition to covering the analysis of whole genome shotgun sequencing data, the course has also module on community analysis of...

Scientific topics: Metagenomics

Resource type: Video, course materials

Metagenomics data analysis https://tess.elixir-europe.org/materials/metagenomics-data-analysis This course covers metagenomics analysis from quality control, filtering and assembly to taxonomic classification, functional assignment and comparative metagenomics. In addition to covering the analysis of whole genome shotgun sequencing data, the course has also module on community analysis of amplicon sequencing data (16S rRNA). Finally, international databases and standards for storing the data are introduced. The course material includes slides, exercises and lecture videos. The workshop is organized in collaboration with the ELIXIR EXCELERATE project and PRACE, and it is part of the PRACE Advanced Training Centre activity. Eija Korpelainen Metagenomics
BBSRC: Data and Data Visualisation

Michael Ball from BBSRC's closing remarks on Data and Data Visualisation from 1st BiVi in 2014. Created at: 1st BiVi Annual Meeting.

Scientific topics: Phylogenetics, Pathway or network

Keywords: Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations, Information visualisation

Resource type: Video

BBSRC: Data and Data Visualisation https://tess.elixir-europe.org/materials/bbsrc-data-and-data-visualisation Michael Ball from BBSRC's closing remarks on Data and Data Visualisation from 1st BiVi in 2014. Created at: 1st BiVi Annual Meeting. Michael Ball Phylogenetics Pathway or network Anatomy Physiology and Atlases, Cells and Organisms, Genome, Molecular, Pathway, Phylogenetics, Populations, Information visualisation 2017-02-01
MARender: A Simple JavaScript Library for Biomedical Visualisation

Bill Hill and Richard Baldock describe MARender, a simple JavaScipt library for biomedical visualisation at 2nd BiVi in 2015.  Created at: 2nd BiVi Annual Meeting.

Keywords: Anatomy Physiology and Atlases, Information visualisation

Resource type: Slideshow

MARender: A Simple JavaScript Library for Biomedical Visualisation https://tess.elixir-europe.org/materials/marender-a-simple-javascript-library-for-biomedical-visualisation Bill Hill and Richard Baldock describe MARender, a simple JavaScipt library for biomedical visualisation at 2nd BiVi in 2015.  Created at: 2nd BiVi Annual Meeting. Mr. William Edward Hill Anatomy Physiology and Atlases, Information visualisation 2017-02-03
SeqMonk: Using visualisation to identify errors and biases in genome scale sequencing data

The increasing scale and complexity of genome scale studies has led to more widespread use of unsupervised analysis pipelines and reduced inspection and sanity checking of the underlying data.  Here we will illustrate how the use of interactive visualisation tools along with an explorative...

Keywords: Genome

Resource type: Video

SeqMonk: Using visualisation to identify errors and biases in genome scale sequencing data https://tess.elixir-europe.org/materials/seqmonk-using-visualisation-to-identify-errors-and-biases-in-genome-scale-sequencing-data The increasing scale and complexity of genome scale studies has led to more widespread use of unsupervised analysis pipelines and reduced inspection and sanity checking of the underlying data.  Here we will illustrate how the use of interactive visualisation tools along with an explorative approach to analysis can identify problems which would otherwise go undetected by standard pipelines. Created at: 3rd BiVi Annual Meeting (2017). Dr. Simon Andrews Genome 2017-05-15