Isaac Virshup ivirshup
ivirshup
/ polygons_on_points.py
Last active
February 24, 2023 12:26
spatial aggregations w polygons
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| import pandas as pd | |
| import geopandas as gpd | |
| import numpy as np | |
| from scipy import sparse | |
| import anndata as ad | |
| def aggregate_polygons_on_points( | |
| polygons: gpd.GeoDataFrame, | |
| points: gpd.GeoDataFrame, | |
| point_id_column: str, |
ivirshup
/ transcript_models.py
Last active
February 13, 2023 15:55
Getting the transcript models out of the bioconductor ensdb tables and turning them into an awkward array
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| import ibis | |
| import awkward as ak | |
| !wget https://bioconductorhubs.blob.core.windows.net/annotationhub/AHEnsDbs/v108/EnsDb.Hsapiens.v108.sqlite | |
| connection = ibis.sqlite.connect("EnsDb.Hsapiens.v108.sqlite") | |
| gene = connection.table("gene") | |
| tx = connection.table("tx") | |
| tx2exon = connection.table("tx2exon") |
ivirshup
/ 01_scrape-dependent-packages-from-wheelodex.ipynb
Created
November 16, 2022 16:17
scverse core dependent packages
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ivirshup
/ mmap_csr_sparse.ipynb
Last active
November 8, 2022 10:50
Example code for reading from a memory mapped sparse array
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ivirshup
/ cellxgenedp_example.ipynb
Last active
October 5, 2023 15:35
Downloading an h5ad file from cellxgene API
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ivirshup
/ scverse-core_github-dependents.ipynb
Last active
October 10, 2022 18:22
Notebook for getting scverse core packages dependents from github
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ivirshup
/ scverse-core_pypi-dependents.ipynb
Created
October 10, 2022 17:56
Notebook for getting scverse core packages pypi dependents from wheelodex
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ivirshup
/ anndata_dask_df.py
Created
September 2, 2022 14:07
anndata dataframe -> dask with columnar support
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| import copy | |
| import dask.dataframe as dd | |
| import dask.array as da | |
| import dask | |
| from dask.base import tokenize | |
| from dask.dataframe.io.io import from_map | |
| import pandas as pd, numpy as np, zarr |
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