# evo_missense

**Repository Path**: larryivanhan/evo_missense

## Basic Information

- **Project Name**: evo_missense
- **Description**: No description available
- **Primary Language**: Unknown
- **License**: Not specified
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2026-06-26
- **Last Updated**: 2026-06-26

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# Evo-missense

Reproducibility package and manuscript analysis code for:

**Mammalian evolutionary observability stratifies predicted human missense effects**

The repository is organized so reviewers can rebuild analysis tables from public raw data, then render the manuscript figures.

## Quick Start

```bash
conda env create -f repro/envs/environment.yml
conda activate evo-missense-repro
cd code
bash ../repro/scripts/run_all.sh --mode full --threads 8
```

For a lightweight software-path test:

```bash
conda activate evo-missense-repro
cd code
bash ../repro/scripts/run_all.sh --mode smoke --threads 4
```

See [repro/README.md](repro/README.md) for raw data URLs, pipeline stages, and expected outputs.

## Repository Contents

- `repro/`: raw-to-results workflow, conda environment, configuration, and smoke fixture.
- `code/scripts/`: R and Python scripts used to render the manuscript figures and structural views.
- `code/assets/`: small static figure assets needed by the figure scripts.
- `code/*.tsv`, `code/fig1/`: compact figure-ready summary tables and a workflow panel retained for convenience.

Large public raw files and derived intermediates are intentionally not tracked. They are downloaded or regenerated by the reproducibility workflow.