Instructions_for_Loading_HDF5_Files.txt

##instructions for loading a scRNA-seq dataset in HDF5 (.h5) format into "scanpy" using ipython

1. enter "ipython" on command line to enter.
2. "import scanpy as sc"
3. download the .h5 file into your directory of choice.
4."adata = sc.read_10x_h5('filename', genome=None, gex_only=True, backup_url=None)"

##you will receive a warning about '.var_names_make_unique'

5."adata.var_names_make_unique()

##you can now conduct various scanpy calculations and generate plots. Browse this website for instructions on how to use these functions. https://scanpy.readthedocs.io/en/latest/generated/scanpy.pl.heatmap.html