Register training material
10 materials found

Related resources: Proteomics dataset  or Transcriptomics dataset 


Transcriptomics - CLIP-Seq data analysis from pre-processing to motif detection

Training material for all kinds of transcriptomics analysis.

Questions of the tutorial:

  • How is raw CLIP-Seq data processed and analysed?
  • How do I find binding motifs and targets for a protein (e.g., RBFOX2)?

Objectives of the tutorial:

  • Remove Adapters, Barcodes and Unique Molecular...

Resource type: Tutorial

Transcriptomics - Visualization of RNA-Seq results with CummeRbund

Training material for all kinds of transcriptomics analysis.

Questions of the tutorial:

  • How are RNA-Seq results stored?
  • Why are visualization techniques needed?
  • How to select our desired subjects for differential gene expression analysis?

Objectives of the tutorial:

  • Manage RNA-Seq...

Resource type: Tutorial

Proteomics - Peptide and Protein ID using OpenMS tools

Training material for proteomics workflows in Galaxy

Questions of the tutorial:

  • How to convert LC-MS/MS raw files?
  • How to identify peptides?
  • How to identify proteins?
  • How to evaluate the results?

Objectives of the tutorial:

  • Protein identification from LC-MS/MS raw files.

Resource type: Tutorial

Transcriptomics - Reference-based RNA-Seq data analysis

Training material for all kinds of transcriptomics analysis.

Questions of the tutorial:

  • What are the effects of Pasilla (PS) gene depletion on splicing events?
  • How to analyze RNA sequencing data using a reference genome?

Objectives of the tutorial:

  • Analysis of RNA sequencing data using...

Resource type: Tutorial

Transcriptomics - Differential abundance testing of small RNAs

Training material for all kinds of transcriptomics analysis.

Questions of the tutorial:

  • What small RNAs are expressed?
  • What RNA features have significantly different numbers of small RNAs targeting them between two conditions?

Objectives of the tutorial:

  • Process small RNA-seq datasets...

Resource type: Tutorial

Transcriptomics - De novo transcriptome reconstruction with RNA-Seq

Training material for all kinds of transcriptomics analysis.

Questions of the tutorial:

  • What genes are differentially expressed between G1E cells and megakaryocytes?
  • How can we generate a transcriptome de novo from RNA sequencing data?

Objectives of the tutorial:

  • Analysis of RNA...

Resource type: Tutorial

Proteomics - Peptide and Protein Quantification via Stable Isotope Labelling (SIL)

Training material for proteomics workflows in Galaxy

Questions of the tutorial:

  • What are MS1 features?
  • How to quantify based on MS1 features?
  • How to map MS1 features to MS2 identifications?
  • How to evaluate and optimize the results?

Objectives of the tutorial:

  • MS1 feature...

Resource type: Tutorial

Proteomics - Peptide and Protein ID using SearchGUI and PeptideShaker

Training material for proteomics workflows in Galaxy

Questions of the tutorial:

  • How to convert LC-MS/MS raw files?
  • How to identify peptides?
  • How to identify proteins?
  • How to evaluate the results?

Objectives of the tutorial:

  • Protein identification from LC-MS/MS raw files.

Resource type: Tutorial

Proteomics - Secretome Prediction

Training material for proteomics workflows in Galaxy

Questions of the tutorial:

  • How to predict cellular protein localization based upon GO-terms?
  • How to combine multiple localization predictions?

Objectives of the tutorial:

  • Predict proteins in the cellular secretome by using...

Resource type: Tutorial

Proteomics - Metaproteomics tutorial

Training material for proteomics workflows in Galaxy

Questions of the tutorial:

  • How can I match metaproteomic mass spectrometry data to peptide sequences derived from shotgun metagenomic data?
  • How can I perform taxonomy analysis and visualize metaproteomics data?
  • How can I perform...

Resource type: Tutorial