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...
Transcriptomics - CLIP-Seq data analysis from pre-processing to motif detection
http://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/clipseq/tutorial.html
http://tess.elixir-uk.org/materials/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 Identifiers (UMIs) from the reads
- Align trimmed reads with STAR
- De-duplicate the read library
- Inspect the read mapping and de-duplication quality
- Perform peak calling with PEAKachu
- Analyse the peaks and find potential binding motifs and targets
- Check the quality of the peak calling
Florian-H-Lab
dmaticzka
bebatut
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...
Transcriptomics - Visualization of RNA-Seq results with CummeRbund
http://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/rna-seq-viz-with-cummerbund/tutorial.html
http://tess.elixir-uk.org/materials/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 results
- Extract the desired subject for differential gene expression analysis
- Visualize information
bagnacan
Introduction to Galaxy Analyses - From peaks to genes
Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.
Questions of the tutorial:
- How to use Galaxy?
- How to get...
Introduction to Galaxy Analyses - From peaks to genes
http://galaxyproject.github.io/training-material/topics/introduction/tutorials/galaxy-intro-peaks2genes/tutorial.html
http://tess.elixir-uk.org/materials/galaxy-introduction-from-peaks-to-genes
Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming experience.
Questions of the tutorial:
- How to use Galaxy?
- How to get from peak regions to a list of gene names?
Objectives of the tutorial:
- Familiarize yourself with the basics of Galaxy
- Learn how to obtain data from external sources
- Learn how to run tools
- Learn how histories work
- Learn how to create a workflow
- Learn how to share your work
pajanne
blankclemens
bebatut
bgruening
nsoranzo
dyusuf
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...
Transcriptomics - Reference-based RNA-Seq data analysis
http://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html
http://tess.elixir-uk.org/materials/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 a reference genome
- Analysis of differentially expressed genes
- Identification of functional enrichment among differentially expressed genes
bebatut
malloryfreeberg
moheydarian
erxleben
pavanvidem
blankclemens
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...
Transcriptomics - Differential abundance testing of small RNAs
http://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/srna/tutorial.html
http://tess.elixir-uk.org/materials/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 to determine quality and reproducibility.
- Filter out contaminants (e.g. rRNA reads) in small RNA-seq datasets.
- Differentiate between subclasses of small RNAs based on their characteristics.
- Identify differently abundant small RNAs and their targets.
malloryfreeberg
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...
Transcriptomics - De novo transcriptome reconstruction with RNA-Seq
http://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/de-novo/tutorial.html
http://tess.elixir-uk.org/materials/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 sequencing data using a reference genome
- Reconstruction of transcripts without reference transcriptome (de novo)
- Analysis of differentially expressed genes
malloryfreeberg
moheydarian
