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1. Seurat_SCT_v._Log Seurat_SCT_v._Log Public

   Comparison of Seurat normalization workflows and manual vs. SeuratData cluster labeling on the PBMC3k dataset.

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2. Monocle_3 Monocle_3 Public

   Single-cell RNA-seq trajectory analysis using Monocle 3 with C. elegans embryo and L2 larval data from the Trapnell lab.

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3. MNIST_CC MNIST_CC Public

   A simple neural net Python script for training on the MNIST dataset given to Claude Code with instructions to significantly improve the model.

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4. Scanpy_Bone_Marrow Scanpy_Bone_Marrow Public

   Single-cell RNA-seq analysis of the human bone marrow samples using the Scanpy framework, following the scverse tutorials.

   Jupyter Notebook

5. Scanpy_Ingest_BBKNN Scanpy_Ingest_BBKNN Public

   Single-cell RNA-seq data integration using Scanpy's ingest() and BBKNN, demonstrates PCA-based label transfer and batch correction on PBMC and pancreas datasets.

   Jupyter Notebook

6. Scanpy_Trajectory_Inference_Hematopoiesis Scanpy_Trajectory_Inference_Hematopoiesis Public

   Trajectory inference for mouse hematopoiesis using Scanpy's PAGA workflow. Reconstructs myeloid and erythroid differentiation paths from the Paul et al. (2015) bone marrow dataset, with graph denoi…

   Jupyter Notebook