README.md

In MahShaaban/curatedAdipoArray: A Curated Microarrays Dataset of MDI-induced Differentiated Adipocytes (3T3-L1) Under Genetic and Pharmacological Perturbations

curatedAdipoArray

A Curated Microarrays Dataset of MDI-induced Differentiated Adipocytes (3T3-L1) Under Genetic and Pharmacological Perturbations

Overview

A curated dataset of Microarrays samples. The samples are MDI-induced pre- adipocytes (3T3-L1) at different time points/stage of differentiation under different types of genetic (knockdown/overexpression) and pharmacological (drug treatment). The package documents the data collection and processing. In addition to the documentation, the package contains the scripts that was used to generated the data.

Introduction

What is curatedAdipoArray?

This package is for documenting and distributing a curated dataset of gene expression from MDI-induced 3T3-L1 adipocyte cell model under genetic and pharmacological modification.

What is contained in curatedAdipoArray?

The package contains two things:

1. Scripts for documenting and reproducing the dataset in inst/scripts.
2. Access to the clean and the processed data SummarizedExperiment objects through ExperimentHub.

What is curatedAdipoArray for?

The data contained in the package can be used in any number of downstream analysis such as differential expression and gene set enrichment.

Installation

The curatedAdipoArray package can be installed from Bioconductor using BiocManager.

```{r install_biocmanager,eval=FALSE} if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("curatedAdipoArray")

# 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_array:latest

# Citing `curatedAdipoArray`

To cite the package use:

```{r citation, eval=FALSE}
# citing the package
citation("curatedAdipoArray")

MahShaaban/curatedAdipoArray documentation built on Feb. 16, 2020, 2:30 a.m.