https://github.com/gersteinlab/hisnuc
https://github.com/gersteinlab/hisnuc
Last synced: 9 months ago
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- Host: GitHub
- URL: https://github.com/gersteinlab/hisnuc
- Owner: gersteinlab
- License: mit
- Created: 2025-08-26T15:24:40.000Z (9 months ago)
- Default Branch: main
- Last Pushed: 2025-08-27T00:18:46.000Z (9 months ago)
- Last Synced: 2025-08-27T08:03:22.039Z (9 months ago)
- Language: Python
- Size: 47 MB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# HISNUC
# Data resources:
QuPath extracted nuclear feature:
A. summary statistics of nuclear features are available for download here:
[`summary statistics (Supplementary Data 1)`](qupath-nuclear-feature-summary-statistics.zip)
Raw nucleus features extracted by QuPath for each tissue are available for download here:
(1) [`Tibial artery`](https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fs3.amazonaws.com%2Forg.gersteinlab.archive.pub%2Fpapers%2Fgtex-nuc-features%2Fqupath-artery-tibial.tar.gz&data=05%7C02%7Cran.meng%40yale.edu%7Ca8e8fee1137a4fd3a87908dce547cbf5%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C638637344316797767%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=wPU0wgh%2F%2BKqn76MyPtFUODWBP8x%2F37hLChrasSG1R2Q%3D&reserved=0feature)
(2) [`Thyroid`](https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fs3.amazonaws.com%2Forg.gersteinlab.archive.pub%2Fpapers%2Fgtex-nuc-features%2Fqupath-thyroid.tar.gz&data=05%7C02%7Cran.meng%40yale.edu%7Ca8e8fee1137a4fd3a87908dce547cbf5%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C638637344316814378%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=oLVAkr3zWn7rRGRc10cm8e4tIyeYQYtqDYwkztD0rwc%3D&reserved=0)
(3)[`nerve-tibial`](https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fs3.amazonaws.com%2Forg.gersteinlab.archive.pub%2Fpapers%2Fgtex-nuc-features%2Fqupath-nerve-tibial.tar.gz&data=05%7C02%7Cran.meng%40yale.edu%7Ca8e8fee1137a4fd3a87908dce547cbf5%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C638637344316825906%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=XsiK0tYZbRV%2F%2FCcidcjsrOzyenP%2Fy1nW41ftv16Dv7U%3D&reserved=0)
(4)[`skin-not-exposed`](https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fs3.amazonaws.com%2Forg.gersteinlab.archive.pub%2Fpapers%2Fgtex-nuc-features%2Fqupath-skin-not-exposed.tar.gz&data=05%7C02%7Cran.meng%40yale.edu%7Ca8e8fee1137a4fd3a87908dce547cbf5%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C638637344316837220%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=DWsHezNejzPHZfetjES7jO3X3epGVEcyFCFEhjjS1S4%3D&reserved=0)
(5)[`skin-sun-exposed`](https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fs3.amazonaws.com%2Forg.gersteinlab.archive.pub%2Fpapers%2Fgtex-nuc-features%2Fqupath-skin-sun-exposed.tar.gz&data=05%7C02%7Cran.meng%40yale.edu%7Ca8e8fee1137a4fd3a87908dce547cbf5%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C638637344316848272%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=CY030%2BFlG8X8c67YMAqHJFiNTmz%2Fa3aKHASu2khUU20%3D&reserved=0)
(6) [`heart-left-ventricle`](https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fs3.amazonaws.com%2Forg.gersteinlab.archive.pub%2Fpapers%2Fgtex-nuc-features%2Fqupath-heart-leftventricle.tar.gz&data=05%7C02%7Cran.meng%40yale.edu%7Ca8e8fee1137a4fd3a87908dce547cbf5%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C638637344316861912%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=Kp4lNsSRs4c48jwGEGVH1zb5xXVrqMkvxFp9grxUJUg%3D&reserved=0)
(7)[`lung`](https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fs3.amazonaws.com%2Forg.gersteinlab.archive.pub%2Fpapers%2Fgtex-nuc-features%2Fqupath-lung.tar.gz&data=05%7C02%7Cran.meng%40yale.edu%7Ca8e8fee1137a4fd3a87908dce547cbf5%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C638637344316873406%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=k51bRc%2FWJV%2BT1O%2B%2FIuHIaQjG0It1e0mm2TyngvyeU7A%3D&reserved=0)
(8) [`muscle`](https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fs3.amazonaws.com%2Forg.gersteinlab.archive.pub%2Fpapers%2Fgtex-nuc-features%2Fqupath-muscle.tar.gz&data=05%7C02%7Cran.meng%40yale.edu%7Ca8e8fee1137a4fd3a87908dce547cbf5%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C638637344316884651%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=gCHnmJxpHfqZeAtdEfCrmjceTlBasKbanqo%2B7lysruY%3D&reserved=0)
(9) [`esophagus-mucosa`](https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fs3.amazonaws.com%2Forg.gersteinlab.archive.pub%2Fpapers%2Fgtex-nuc-features%2Fqupath-esophagus-mucosa.gz&data=05%7C02%7Cran.meng%40yale.edu%7Ca8e8fee1137a4fd3a87908dce547cbf5%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C638637344316895953%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=TUpBfeDdMaT0PkPWqrY6wuvoz2rZETFjldcp3CapYeE%3D&reserved=0)
(10) [`muscularis`](https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fs3.amazonaws.com%2Forg.gersteinlab.archive.pub%2Fpapers%2Fgtex-nuc-features%2Fqupath-esophagus-muscularis.tar.gz&data=05%7C02%7Cran.meng%40yale.edu%7Ca8e8fee1137a4fd3a87908dce547cbf5%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C638637344316907144%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=7zz9nK%2BZM8FjKuCiN1kgomvzF2xnvaUCQjH1KKcJU9s%3D&reserved=0)
(11) [`heart-atrail-appendages`](https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fs3.amazonaws.com%2Forg.gersteinlab.archive.pub%2Fpapers%2Fgtex-nuc-features%2Fqupath-heart-atrial-appendages.tar.gz&data=05%7C02%7Cran.meng%40yale.edu%7Ca8e8fee1137a4fd3a87908dce547cbf5%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C638637344316918277%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=yPZ6IQlDxWbNTCNCqbLsYlt1nNDT5uS8NUDbdVzQVtQ%3D&reserved=0)
(12)[`artery-tibial`](https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fs3.amazonaws.com%2Forg.gersteinlab.archive.pub%2Fpapers%2Fgtex-nuc-features%2Fqupath-artery-tibial.tar.gz&data=05%7C02%7Cran.meng%40yale.edu%7Ca8e8fee1137a4fd3a87908dce547cbf5%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C638637344316929421%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=dDkGRGodFjRQnCBNA8ZMhm64jDlsqK7o0ldhxvDmUlk%3D&reserved=0)
ImageQTL results with LD prunned using FUMA are available here: [`ImageQTL (Supplementary Data 2)`](ImageQTL-FUMA-result.zip)
DE genes results are splitted into three parts due to file size limitations. [`DEgenes1`](DE_genes_part1.zip)[`DEgenes2`](DE_genes_part2.zip)[`DEgenes3`](DE_genes_part3.zip)
EWAS results (only for lung tissues) [`EWAS-lung`](EWAS.zip)
# Code resources:
HISNUC-X model code:[`HISNUC-X-code`](https://github.com/gersteinlab/HISNUC/tree/main/HISNUC-X)
HISNUC-X trained 12 models: [`HISNUC-X-models`](https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fs3.us-east-1.amazonaws.com%2Forg.gersteinlab.archive.pub%2Fpapers%2Fgtex-imaging-data%2FHISNUC-X-model.zip&data=05%7C02%7Cran.meng%40yale.edu%7C919153f1d7774300aa4c08dd0d6b140a%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C638681476596549069%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=O1l6Pt3jiDzOokHBmrtQi92uaxIDX9fuuySmmayKBYg%3D&reserved=0)
HISNUC-Age model code: [`HISNUC-Age-code`](https://github.com/gersteinlab/HISNUC/tree/main/HISNUC-AGE)
HISNUC-Age trained 12 models : [`HISNUC-Age-models`](https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fs3.us-east-1.amazonaws.com%2Forg.gersteinlab.archive.pub%2Fpapers%2Fgtex-imaging-data%2FHISNUC-Age-model.zip&data=05%7C02%7Cran.meng%40yale.edu%7C919153f1d7774300aa4c08dd0d6b140a%7Cdd8cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C638681476596525546%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=qkHbP%2BJnsErwvk8XkB6CBSTwjSnGY%2BvQKq8RpFRE3yk%3D&reserved=0)