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| """ | |
| Generate AnnData fro DF or H5AD | |
| """ | |
| import scanpy as sc | |
| import anndata | |
| ad=anndata.AnnData(X=input.X, obs=input.obs, var=input.var) | |
| ad.var_names_make_unique() | |
| ad |
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| """ | |
| Selection of useful jupyter notebook commands | |
| """ | |
| # control plot size | |
| import matplotlib.pyplot as plt | |
| plt.rcParams['figure.figsize'] = [10, 5] | |
| # autoreload code dependencies with each run | |
| %load_ext autoreload |
rgranit
/ hypergeometric.py
Last active
April 23, 2020 19:42
Hypergeometric test for gene list overlap in python
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| """ | |
| The aim of this script is to test the significance of gene list overlap | |
| """ | |
| # load packages | |
| import scipy.stats as stats | |
| from decimal import Decimal as D | |
| def overlap_sets(setA, setB): |