PeakyFinders/README.Rmd at master · neurogenomics/PeakyFinders · GitHub

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---
title: ""
author: "`r rworkflows::use_badges()`"
date: "<h4>README updated: <i>`r format( Sys.Date(), '%b-%d-%Y')`</i></h4>"
output:
  github_document
---

```{r, echo=FALSE, include=FALSE}
pkg <- read.dcf("DESCRIPTION", fields = "Package")[1]
title <- read.dcf("DESCRIPTION", fields = "Title")[1]
description <- read.dcf("DESCRIPTION", fields = "Description")[1]
URL <- read.dcf('DESCRIPTION', fields = 'URL')[1]
owner <- tolower(strsplit(URL,"/")[[1]][4])
```

## `r pkg`: `r title`

`r description`

### Key Features

- **Multi-source import**: Fetch peaks from GEO, ENCODE, ROADMAP, and AnnotationHub with a single function
- **Automatic peak calling**: When peak files aren't available, automatically calls peaks from bedGraph or bigWig files using MACS3 or SEACR
- **Region filtering**: Import only peaks overlapping regions of interest
- **Genome build handling**: Automatic liftOver between genome builds (hg19/hg38)
- **Parallelisation**: Efficiently import multiple peak files in parallel

## Installation

```R
if(!require("BiocManager")) install.packages("BiocManager")

BiocManager::install("`r owner`/`r pkg`")
library(`r pkg`)
```

## Quick Start

```R
library(PeakyFinders)

# Import peaks from multiple sources at once
ids <- c(
    "GSM945244",    # GEO
    "ENCSR000AHD",  # ENCODE
    "AH32001"       # AnnotationHub
)

peaks <- import_peaks(
    ids = ids,
    builds = "hg38",
    searches = list(narrowPeak = "narrowpeak")
)

# Filter to a specific region
query_region <- GenomicRanges::GRanges("chr22:1-50000000")
peaks_filtered <- import_peaks(
    ids = ids,
    builds = "hg38",
    query_granges = query_region,
    query_granges_build = "hg38"
)

# Search for available datasets
encode_metadata <- search_encode(
    target = "H3K27ac",
    biosample = "K562"
)
```

## Documentation

### [Website](https://`r owner`.github.io/`r pkg`)
### [Getting started](https://`r owner`.github.io/`r pkg`/articles/peakyfinders)

## Citation

If you use `r pkg`, please cite:

> `r utils::citation(pkg)$textVersion`

<hr>

## Contact

### [Neurogenomics Lab](https://www.neurogenomics.co.uk/)

UK Dementia Research Institute
Department of Brain Sciences
Faculty of Medicine
Imperial College London
[GitHub](https://github.com/neurogenomics)
[DockerHub](https://hub.docker.com/orgs/neurogenomicslab)

<br>