diff --git a/Single-Cell RNA-seq Clustering Analysis Notebook.ipynb b/Single-Cell RNA-seq Clustering Analysis Notebook.ipynb index 04fffd7..117aa58 100644 --- a/Single-Cell RNA-seq Clustering Analysis Notebook.ipynb +++ b/Single-Cell RNA-seq Clustering Analysis Notebook.ipynb @@ -20,19 +20,19 @@ "\n", "### Analysis Overview\n", "\n", - "1. **Setup Analysis**\n", + "1. [**Setup Analysis**](#Step-1:-Setup-Analysis)\n", " 1. Load raw count matrix.\n", - "2. **Preprocess Counts**\n", + "2. [**Preprocess Counts**](#Step-2:-Preprocess-Counts)\n", " 1. Filter cells based on QC metrics.\n", " 2. Perform data normalization and scaling.\n", " 3. Remove unwanted sources of variation (number of detected molecules per cell as well as the percentage mitochondrial gene content).\n", " 4. Detect highly variable genes.\n", " 5. Perform linear dimensional reduction (PCA).\n", - "3. **Cluster Cells**\n", + "3. [**Cluster Cells**](#Step-3:-Cluster-Cells)\n", " 1. Cluster cells (graph-based clustering) in PCA space and visualize using t-SNE.\n", - "4. **Visualize Cluster Markers**\n", + "4. [**Visualize Cluster Markers**](#Step-4:-Visualize-Cluster-Markers)\n", " 1. Explore and visualize cluster markers interactively.\n", - "5. **Export Analysis Data**\n", + "5. [**Export Analysis Data**](#Step-5:-Export-Analysis-Data)\n", " 1. Export data to `.csv` files or a compressed `.h5ad` format." ] }, diff --git a/__init__.py b/__init__.py new file mode 100644 index 0000000..e69de29