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Update ATAC notebooks#9

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jordanc17 wants to merge 4 commits intosettylab:mainfrom
jordanc17:cailin-atac-update
Open

Update ATAC notebooks#9
jordanc17 wants to merge 4 commits intosettylab:mainfrom
jordanc17:cailin-atac-update

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@jordanc17
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@jordanc17 jordanc17 commented Mar 19, 2025

I completed the following steps:

  • Added renv files for ArchR
  • updated the script to make it more easily reusable
  • updated ATAC stand-alone notebook
  • Moved coverage plots to their own notebook.

Remaining to-dos:

  • Sync settylab/ArchR fork
  • If desired, update coverage plot notebook to use pyGenomeTracks or another pre-existing package for easier re-use.
  • Make comparable script for Signac analysis to move away from ArchR

@jordanc17 jordanc17 requested a review from ManuSetty March 19, 2025 00:35
@jordanc17 jordanc17 self-assigned this Mar 19, 2025
"File \u001b[0;32m~/.conda/envs/singlecell/lib/python3.8/site-packages/pandas/_libs/index.pyx:163\u001b[0m, in \u001b[0;36mpandas._libs.index.IndexEngine.get_loc\u001b[0;34m()\u001b[0m\n",
"File \u001b[0;32mpandas/_libs/hashtable_class_helper.pxi:5198\u001b[0m, in \u001b[0;36mpandas._libs.hashtable.PyObjectHashTable.get_item\u001b[0;34m()\u001b[0m\n",
"File \u001b[0;32mpandas/_libs/hashtable_class_helper.pxi:5206\u001b[0m, in \u001b[0;36mpandas._libs.hashtable.PyObjectHashTable.get_item\u001b[0;34m()\u001b[0m\n",
"\u001b[0;31mKeyError\u001b[0m: 'phenograph'",
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Looks like the notebook did not run through and failed here. Maybe needs a fix and rerun.

"Hash": "a85c767b55f0bf9b7ad16c6d7baee5bb",
"Requirements": []
}
}
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How come ArchR is not part of the renv?

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not sure, it should be. Let me double-check and make sure everything's properly recorded in the lockfile.

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