Downstream processing of RNA-Seq data in GenePattern

  • Run RNA-seq downstream processing analyses in GenePattern, such as clustering, classification, GSEA...
  • Use GenePattern to save workflows, ensure reproducibility and share methodologies with colleagues and reviewers
  • Use the GenePattern Notebook environment to create documents that interleave formatted text, graphics and other multimedia, executable code, and GenePattern analyses, creating a single "research narrative" that puts scientific discussion and analyses in the same place

Summary
The workshop will cover the use of GenePattern for downstream processing of high-throughput mRNA sequencing (RNA-Seq) data produced by Illumina sequencing machines.  This workshop is intended for non-programming biologists.

  1. Running Analyses in GenePattern
  2. Clustering
  3. Prediction and Clasification
  4. Working with analysis workflows: GenePattern pipelines
  5. Working with Samples and Features
  6. The GenePattern Notebook environment
  7. Related tools: IGV, GSEA
  8. Open Q&A

The data files, slides and exercises will be made available after the workshop.
 

Scientific topics: RNA-Seq

Target audience: Life Science Researchers, PhD students, post-docs

Authors: Barbara Hill Meyers and Michael Reich

Remote created date: 2016-04-22

Remote updated date: 2017-10-09

Downstream processing of RNA-Seq data in GenePattern https://tess.elixir-europe.org/materials/downstream-processing-of-rna-seq-data-in-genepattern - Run RNA-seq downstream processing analyses in GenePattern, such as clustering, classification, GSEA... - Use GenePattern to save workflows, ensure reproducibility and share methodologies with colleagues and reviewers - Use the GenePattern Notebook environment to create documents that interleave formatted text, graphics and other multimedia, executable code, and GenePattern analyses, creating a single "research narrative" that puts scientific discussion and analyses in the same place Summary The workshop will cover the use of GenePattern for downstream processing of high-throughput mRNA sequencing (RNA-Seq) data produced by Illumina sequencing machines.  This workshop is intended for non-programming biologists. 1. Running Analyses in GenePattern 2. Clustering 3. Prediction and Clasification 4. Working with analysis workflows: GenePattern pipelines 5. Working with Samples and Features 6. The GenePattern Notebook environment 7. Related tools: IGV, GSEA 8. Open Q&A The data files, slides and exercises will be made available after the workshop.   RNA-Seq Life Science Researchers PhD students post-docs 2016-04-22 2017-10-09