scanpy-demo-czbiohub

This is the github repositiory of the 2-day workshop on single-cell RNA-seq data analysis taken place at the CZ Biohub in San Francisco on 10/31 - 11/1/19.

Data for the general introductory tutorial on 4k PBMCs from 10X genomics:

Demo dataset comes originally from 10X Genomics, available in various formats here: https://support.10xgenomics.com/single-cell-gene-expression/datasets/1.2.0/pbmc4k The demo dataset of the tutorial is made available via Gigamove (link works until 11/11/19): https://gigamove.rz.rwth-aachen.de/d/id/xDALfiSFawCCcz

Introduction to differential tests

Tutorials are found in https://github.com/theislab/diffxpy_tutorials.

Introduction to velocities

Here, we work on the dynamical velocity model of Bergen et al. on bioRxiv (https://www.biorxiv.org/content/10.1101/820936v1) Please follow the link to the package: https://github.com/theislab/scvelo We will use the following demo notebooks: https://scvelo-notebooks.readthedocs.io/DentateGyrus.html and https://scvelo-notebooks.readthedocs.io/Pancreas.html or as jupyter notebooks https://github.com/theislab/scvelo_notebooks/blob/master/DentateGyrus.ipynb and https://github.com/theislab/scvelo_notebooks/blob/master/Pancreas.ipynb.

Google doc for questions

https://docs.google.com/document/d/1t4qFcVByExVxEtN7FUHtuDqObVzrSCfs92mQRgJXBEM/edit?usp=sharing