curatedAdipoChIP

A Curated ChIP-Seq Dataset of MDI-induced Differentiated Adipocytes (3T3-L1)

Overview

In this documnet, we introduce the purpose of curatedAdipoChIP package, its contents and its potential use cases. This package is a curated dataset of ChIP-Seq samples. The samples are MDI-induced pre-adipocytes (3T3-L1) at different time points/stage of differentiation. The ChIP-antibodies used in this dataset are of transcription factors, chromatin remodelers and histone modifications. The package document the data collection, pre-processing and processing. In addition to the documentation the package contains the scripts that were used to generated the data in inst/scripts and the final RangedSummarizedExperiment object in can be accessed through the ExperimentHub.

Introduction

What is curatedAdipoChIP?

It is an R package for documenting and distributing a curated dataset. The package doesn't contain any R functions.

What is contained in curatedAdipoChIP?

The package contains two different things:

1. Scripts for documenting/reproducing the data in inst/scripts
2. Access to a RangedSummarizedExperiment object in through the ExperimentHub.

What is curatedAdipoChIP for?

The RangedSummarizedExperiment object contains the peak_counts, colData, rowRanges and metadata which can be used for the purposes of conducting differential peak binding or gene set enrichment analysis on the cell line model.

Installation

The package can be installed using BiocManager.

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("curatedAdipoChIP")

Docker image

The pre-processing and processing of the data setup environment is available as a docker image. This image is also suitable for reproducing this document. The docker image can be obtained using the docker CLI client.

$ docker pull bcmslab/adiporeg_chip:latest

Citing curatedAdipoChIP

For citing the package use:

# citing the package
citation("curatedAdipoChIP")