Package 'ChIPDBData'

Title: ChIP-seq Target Databases for TFEA.ChIP
Description: Provides curated gene target databases derived from ChIP-seq datasets, formatted as ChIPDB objects for use with TFEA.ChIP.
Authors: Yosra Berrouayel [aut, cre] (ORCID: <https://orcid.org/0000-0002-0768-5933>), Luis del Peso [aut] (ORCID: <https://orcid.org/0000-0003-4014-5688>)
Maintainer: Yosra Berrouayel <[email protected]>
License: GPL-3
Version: 1.2.0
Built: 2026-10-10 11:21:34 UTC
Source: https://github.com/bioc/ChIPDBData

Help Index

Retrieve ChIPDB dataset from ExperimentHub

Description

This function fetches ChIPDB objects (lists of transcription factor–target gene associations) for use with the TFEA.ChIP package. Available datasets include ENCODE, CREDB, and GeneHancer-derived collections.

Usage

getChIPDB(
  name = c("ENCODE_rE2G", "ENCODE_rE2G_25score", "ENCODE_rE2G_50score",
    "ENCODE_rE2G_75score", "ENCODE_rE2G_50depth", "ENCODE_rE2G_100depth",
    "ENCODE_rE2G_200depth", "ENCODE_rE2G_300depth", "CREdb", "GeneHancer")
)

Arguments

name

A character string naming the dataset to retrieve. Options: "ENCODE_rE2G", "ENCODE_rE2G_25score", "ENCODE_rE2G_50score", "ENCODE_rE2G_75score", "ENCODE_rE2G_50depth", "ENCODE_rE2G_100depth", "ENCODE_rE2G_200depth", "ENCODE_rE2G_300depth", "CREdb", "GeneHancer".

Value

A list object of class ChIPDB containing transcription factor–target gene mappings.

Examples

ChIPDB <- getChIPDB("ENCODE_rE2G_300depth")