https://github.com/mahshaaban/curatedadiporna

A Curated RNA-Seq Dataset of MDI-induced Differentiated Adipocytes (3T3-L1)
https://github.com/mahshaaban/curatedadiporna

adipose r rnaseq

Last synced: 4 days ago
JSON representation

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

• Host: GitHub
• URL: https://github.com/mahshaaban/curatedadiporna
• Owner: MahShaaban
• Created: 2019-02-03T09:13:18.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2019-04-19T01:48:12.000Z (over 5 years ago)
• Last Synced: 2023-10-20T21:29:12.546Z (about 1 year ago)
• Topics: adipose, r, rnaseq
• Language: Shell
• Homepage: https://bioconductor.org/packages/curatedAdipoRNA/
• Size: 31.2 MB
• Stars: 0
• Watchers: 2
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

README

        
[![Travis build status](https://travis-ci.org/MahShaaban/curatedAdipoRNA.svg?branch=master)](https://travis-ci.org/MahShaaban/curatedAdipoRNA)

[![AppVeyor build status](https://ci.appveyor.com/api/projects/status/github/MahShaaban/curatedAdipoRNA?branch=master&svg=true)](https://ci.appveyor.com/project/MahShaaban/curatedAdipoRNA)

# 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`.

```{r install_biocmanager,eval=FALSE}

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:

```{r citation, warning=FALSE}

# citing the package

citation("curatedAdipoRNA")

```