Isaac Virshup ivirshup
ivirshup
/ boundaries-to-labels.ipynb
Last active
April 22, 2025 18:03
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| apiVersion: argoproj.io/v1alpha1 | |
| kind: Workflow | |
| metadata: | |
| generateName: census-build-quick | |
| spec: | |
| serviceAccountName: vcp-dev-census-sa | |
| entrypoint: build | |
| VolumeClaimGC: | |
| strategy: OnWorkflowCompletion # delete volume when workflow is done | |
| volumeClaimTemplates: # define volume, same syntax as k8s Pod spec |
ivirshup
/ timing-conversion-from-bed-to-parquet.ipynb
Last active
March 21, 2025 20:35
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We can make this file beautiful and searchable if this error is corrected: It looks like row 2 should actually have 16 columns, instead of 10 in line 1.
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| dataset_id,dataset_asset_h5ad_uri,dataset_version_id,dataset_h5ad_path,dataset_title,citation,collection_id,collection_name,collection_doi,collection_doi_label,asset_h5ad_filesize,cell_count,mean_genes_per_cell,schema_version,dataset_total_cell_count,soma_joinid | |
| f12ab0e6-383c-4362-b1c6-922de09ccbc9,https://datasets.cellxgene.cziscience.com/e092fcfd-0ec0-4109-bcff-146d03da850b.h5ad,e092fcfd-0ec0-4109-bcff-146d03da850b,/mnt/scratch/spatial_soma/source_h5ad/e092fcfd-0ec0-4109-bcff-146d03da850b.h5ad,HTAPP-812-SMP-8239 Slide-seq,Publication: https://doi.org/10.1038/s41591-024-03215-z Dataset Version: https://datasets.cellxgene.cziscience.com/e092fcfd-0ec0-4109-bcff-146d03da850b.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/a96133de-e951-4e2d-ace6-59db8b3bfb1d,a96133de-e951-4e2d-ace6-59db8b3bfb1d,HTAN/HTAPP Broad - Spatio-molecular dissection of the breast cancer metastatic microenvironment,10.1038/s41591-024-03215-z,Klughammer et al. (2024) Nat Me |
ivirshup
/ check-presence-mtx.ipynb
Created
January 28, 2025 03:13
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| b617ee1b-f8c8-4de9-b82b-e803ab93550d | |
| e6e6aec8-c3e4-4e66-8301-e9325528f683 | |
| 686e1a03-54e6-44ec-b9f5-98e3bd75560e |
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| + apt update | |
| WARNING: apt does not have a stable CLI interface. Use with caution in scripts. | |
| Get:1 http://deb.debian.org/debian bookworm InRelease [151 kB] | |
| Get:2 http://deb.debian.org/debian bookworm-updates InRelease [55.4 kB] | |
| Get:3 http://deb.debian.org/debian-security bookworm-security InRelease [48.0 kB] | |
| Get:4 http://deb.debian.org/debian bookworm/main amd64 Packages [8789 kB] | |
| Get:5 http://deb.debian.org/debian bookworm-updates/main amd64 Packages [8856 B] | |
| Get:6 http://deb.debian.org/debian-security bookworm-security/main amd64 Packages [239 kB] | |
| Fetched 9291 kB in 1s (9450 kB/s) | |
| Reading package lists... |
ivirshup
/ author_metadata_census_embeddings.ipynb
Created
December 5, 2024 02:16
ivirshup
/ 05-write-tiledb-from-dask.ipynb
Created
August 14, 2024 20:58
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ivirshup
/ 2024-07-19_demo.ipynb
Last active
July 22, 2024 23:06
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