Metadata-Version: 2.4
Name: QuantNado
Version: 0.1.0
Summary: Quantile-based peak calling from RPKM bigWig files
Author-email: Catherine Chahrour <your.email@example.com>
License-Expression: MIT
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: crested
Requires-Dist: loguru
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: pyranges
Requires-Dist: torch
Provides-Extra: dev
Requires-Dist: pytest; extra == "dev"
Dynamic: license-file

# QuantNado

**QuantNado** is a quantile-based peak caller for CUT&Tag RPKM-scaled bigWig files. It tiles the genome, extracts log1p-transformed signal, and outputs BED files of high-signal regions using quantile thresholding.

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## 📦 Installation

Install using pip:

```bash
pip install quantnado
```

## 🚀 Usage

```bash
QuantNado \
  --bigwig path/to/file.bw \
  --output-dir path/to/output/ \
  --chromsizes path/to/hg38.chrom.sizes \
  # Optional parameters:
  --blacklist path/to/hg38-blacklist.bed \
  --tilesize 128 \
  --quantile 0.98 \
  --min-peak-length 128 \
  --tmp-dir path/to/temp
```
