https://github.com/theislab/scanpy-demo-czbiohub
single-cell scanpy teaching
https://github.com/theislab/scanpy-demo-czbiohub
scanpy single-cell teaching-materials
Last synced: 5 months ago
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single-cell scanpy teaching
- Host: GitHub
- URL: https://github.com/theislab/scanpy-demo-czbiohub
- Owner: theislab
- Created: 2019-10-31T17:31:13.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2019-11-05T03:07:07.000Z (over 6 years ago)
- Last Synced: 2026-01-15T00:52:42.715Z (6 months ago)
- Topics: scanpy, single-cell, teaching-materials
- Language: HTML
- Homepage:
- Size: 9.82 MB
- Stars: 5
- Watchers: 3
- Forks: 5
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# 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