The vignette in this folder demonstrates the ability to load an expression matrix downloaded
from the HCA browser into scanpy and briefly explore the data. The downloaded file, pancreas.loom, is the result of end-to-end processing in the Data Coordination Platform workflow, and is included in this repo.
The file ENSG_to_name.csv contains the Gencode identifiers for the genes in the HCA expression matrices, along with the more commonly used gene symbol (i.e. ENSG00000115263.14,GCG). This might be generally useful in your exploration of HCA expression matrices.
This notebook assumes that you have installed python 3 on your system,
and that the pip executable installs packages for that python
distribution. For some users, it may be necessary to use pip3 instead.
pip install -r requirements.txtDepending on your platform, you might need to install additional depenencies:
$ sudo apt-get install libblas-dev liblapack-dev libatlas-base-dev gfortran libhdf5-dev
$ jupyter notebook hca_demo_scanpy.ipynb