# Upstream helpers for scanpy

The files listed below were recovered from [K-Dense-AI/scientific-agent-skills](https://github.com/K-Dense-AI/scientific-agent-skills) at commit `0936740e52033a6256085be5fc81e5e56d606110`. The repository ID is `1079456184`.

They retain the upstream **MIT** license reproduced in [UPSTREAM-LICENSE.txt](UPSTREAM-LICENSE.txt). This notice applies to the listed support files; it does not replace the license metadata of other catalog files. Preserve the upstream license and this attribution when redistributing them.

License wording is unchanged; text-only trailing whitespace and EOF blank lines are normalized. Original license: https://github.com/K-Dense-AI/scientific-agent-skills/blob/0936740e52033a6256085be5fc81e5e56d606110/LICENSE.md

| Local file | Original upstream path | Original Git blob SHA | Import changes |
| --- | --- | --- | --- |
| `scripts/qc_analysis.py` | `skills/scanpy/scripts/qc_analysis.py` | `45fccd992c4e061129e65a6a215e7e44236c093f` | stored without executable bit; invoke via its interpreter |
| `references/plotting_guide.md` | `skills/scanpy/references/plotting_guide.md` | `3fc4f62075f53c37ad611d0cca5bb64d80cffddb` | text-only trailing whitespace and EOF blank lines normalized |
| `references/standard_workflow.md` | `skills/scanpy/references/standard_workflow.md` | `7184ee932d12c42e9970e0b54f88baf87585ca76` | text-only trailing whitespace and EOF blank lines normalized |
| `references/api_reference.md` | `skills/scanpy/references/api_reference.md` | `40f6659a2b7c32ccb4c2d7ab7e2d14a32f4e2136` | text-only trailing whitespace and EOF blank lines normalized |
| `assets/analysis_template.py` | `skills/scanpy/assets/analysis_template.py` | `fa3d34e3de15a6740974cb1d52f6bd2900ed922d` | content unchanged |