Merge notebooks: remove redundant 01_scanpy_pbmc_workshop.ipynb, update README

Agent-Logs-Url: https://github.com/compbiocore/singlecell_python_workshop/sessions/f3cf2073-2ef1-4688-bf5b-d58bf226a2dc

Co-authored-by: EricSalomaki <6400723+EricSalomaki@users.noreply.github.com>

Author: Copilot

notebooks/01_scanpy_pbmc_workshop.ipynb

@@ -72,9 +72,7 @@ pip install pyhere
 
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-* `01_scanpy_pbmc_workshop.ipynb`: Initial starter workshop notebook for single-cell analysis in Scanpy using the PBMC3k tutorial dataset. Includes an outline plus runnable preprocessing, clustering, and marker gene analysis steps. Paths managed via `pyhere`.
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-* `02_scanpy_pbmc_basics_visualization.ipynb`: Comprehensive beginner workshop notebook for single-cell RNA-seq analysis using Scanpy and the PBMC3k dataset. Covers the full workflow from raw data loading through pathway enrichment. Key sections include:
+* `02_scanpy_pbmc_basics_visualization.ipynb`: Workshop notebook for single-cell RNA-seq analysis using Scanpy and the PBMC3k dataset. Covers the full workflow from raw data loading through pathway enrichment. Key sections include:
   - AnnData data structure introduction
   - Raw data exploration (`sc.pl.highest_expr_genes`)
   - QC metrics, filtering, and doublet detection (Scrublet)