/curatedAdipoRNA

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

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curatedAdipoRNA

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

Overview

In this document, we introduce the purpose of the curatedAdipoRNA package, its contents and its potential use cases. This package is a curated dataset of RNA-Seq samples. The samples are MDI-induced pre-phagocytes (3T3-L1) at different time points/stage of differentiation. The package document the data collection, pre-processing and processing. In addition to the documentation, the package contains the scripts that was used to generated the data in inst/scripts/ and the final RangedSummarizedExperiment object in data/.

Introduction

What is curatedAdipoRNA?

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

What is contained in curatedAdipoRNA?

The package contains two different things:

  1. Scripts for documenting/reproducing the data in inst/scripts
  2. Final RangedSummarizedExperiment object in data/

What is curatedAdipoRNA for?

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

Installation

The curatedAdipoRNA package can be installed from Bioconductor using BiocManager.

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

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_rna:latest

Citing curatedAdipoRNA

For citing the package use:

# citing the package
citation("curatedAdipoRNA")