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An accessible R package to download PulmonDB data
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DESCRIPTION
NAMESPACE
PulmonDB.Rproj
README.md

README.md

title author output vignette
Introduction to PulmonDB
name affiliation
Ana Beatriz Villasenor-Altamirano
Laboratorio Internacional de Investigacion sobre el Genoma Humano (LIIGH), UNAM
name affiliation
Oscar Aldana Assad
Laboratorio Internacional de Investigacion sobre el Genoma Humano (LIIGH), UNAM
name affiliation
Alejandra Medina-Rivera
Laboratorio Internacional de Investigacion sobre el Genoma Humano (LIIGH), UNAM
BiocStyle::html_document
%\VignetteIndexEntry{intro-PulmonDB} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8}

Background

PulmonDB is a gene expression database with Chronic Obstructive Pulmonary Diseases (COPD) and Idiopathic Pulmonary Disease (IPF) experiments. It has homogenized values using individual contrast and manual curated annotation that can be download or accessed by http://pulmondb.liigh.unam.mx.

Setups

library(devtools)

library(PulmonDB)

library(RMySQL)

library(dplyr)

library(tidyr)

library(SummarizedExperiment)

Installation

The package of PulmonDB can be found in Github and intalled by using install_github()

install_github("AnaBVA/PulmonDB")
library(PulmonDB)

Download data

genesPulmonDB()

The aim of this package is to download the data from PulmonDB in R environment for further analysis. The main function is genesPulmonDB , it will give you the homogenized sample contrast values and the annotation as SummarizedExperiment object.


genesPulmonDB(c("MMP1","JUND"),c("GSE1122"))

# End
sessionInfo()
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