This repository contains the code for reproducing all the results and figures in the preprint "Isoform specificity in the mouse primary motor cortex" by A. Sina Booeshaghi, Zizhen Yao, Cindy van Velthoven, Kimberly Smith, Bosiljka Tasic, Hongkui Zeng, and Lior Pachter.

The repo is structured in the following way:

├── analysis
│   ├── notebooks
│   └── scripts
├── data
│   ├── 10xv3
│   ├── merfish
│   ├── notebook
│   └── SMARTseq
├── figures
│   ├── archive
│   └── merfish_subclass_loc
├── notes
├── reference
│   ├── 10xv3_cluster_labels
│   ├── cellranger
│   ├── gencode
│   ├── genome
│   ├── kallisto_index
│   ├── merfish
│   └── smart-seq_cluster_labels
└── tables
    ├── archive
    └── unordered