ELLA

Quick Start

Check out the tutorial pages for demos and documentations to get started with ELLA.

Quick Installation

git clone https://github.com/jadexq/ELLA.git
pip install -r requirements.txt
pip install -e .

Please check out installation for details.

Repo Structure

./ELLA/
├── setup.py % project config
├── requirements.txt % dependencies
├── ELLA % ELLA source code
│   └── ELLA.py
├── docs % source code of the tutorial website
│   ├── ...
├── scripts
│   ├── demo % code and data for the minimum and complete demos
│   │   ├── mini_demo
│   │   └── complete_demo
│   ├── analysis % mRNA characteristic analysis code for each dataset
│   |   ├── merfish1
│   |   ├── seqfish
│   |   ├── seqscope
│   |   └── stereoseq
│   └── preprocessing % data preprocessing code for each data set
│       ├── merfish1
│       ├── seqfish
│       ├── seqscope
│       └── stereoseq
└── README.md

Processed Data

Seq-Scope

• the input that ELLA takes: seqscope_data_dict.pkl
• the registered expression data: seqscope_df_registered_saved.pkl

Stereo-seq

• the input that ELLA takes: stereoseq_data_dict.pkl
• the registered expression data: stereoseq_df_registered_saved.pkl

SeqFISH+

• the input that ELLA takes: seqfish_data_dict.pkl
• the registered expression data: seqfish_df_registered_saved.pkl

Merfish mouse brain

• the input that ELLA takes: merfish_mouse_brain_data_dict.pkl
• the registered expression data: merfish_mouse_brain_df_registered_saved.pkl