CCMI - Workshop

CCMI Software Series: GenePattern Notebooks



9:00 AM-1:00 PM

Michael Reich, Alexander T. Wenzel, Ted Liefeld, Edwin Juarez and Anthony Castanza from Jill Mesirov's lab at UC San Diego will guide us through performing single-cell RNA-seq analyses with the GenePattern Notebook environment

The CCMI’s Computational Biology Software Series will cover a range of publicly available databases and analysis tools to help empower your research.

The GenePattern Notebook environment combines the ease and accessibility of Jupyter Notebooks with the hundreds of genomic analyses available within the GenePattern platform, plus additional features for the easy development and publication of notebooks by scientists at all levels of computational experience. GenePattern makes reproducible research easy: analyses can be rerun at any time with the same inputs; every version of each tool is tracked, so that a result can be reproduced even if the code that produced it changes in the future; and researchers can chain analyses together to encapsulate and share their research as reproducible workflows.

In this hands-on workshop, participants will learn how to use GenePattern Notebooks, with an emphasis on the tools it provides to support the growing field of single-cell RNA-seq analysis. Topics covered will include:

  • Introduction to the GenePattern Notebook environment
  • Formatting and transferring data
  • Single-cell analysis in GenePattern notebooks
  • Preprocessing and clustering with Seurat
  • Cluster harmonization with Conos
  • Upcoming GenePattern Notebook features

The workshop requires no previous experience with GenePattern, but exposure to RNA-seq analysis is helpful. Participants must have an up-to-date web browser.

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