longevityTools: Analysis tools for longevity research

title: "longevityDrugs: Database of Longevity-Associated Drugs (LAD)" author: "Authors: Thomas Girke, Tyler Backman, Dan Evans" date: "Last update: 04 May, 2016" package: "longevityTools 1.0.6" output: BiocStyle::html_document: toc: true toc_depth: 3 fig_caption: yes

fontsize: 14pt bibliography: bibtex.bib

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Introduction

This vignette is part of the NIA funded Longevity Genomics project. For more information on this project please visit its website here. The GitHub repository of the corresponding R package is available here and the most recent version of this vignette can be found here.

The data package longevityDrugs contains molecular structures and annotation information of longevity-associated drugs (LADs). An iterative process will be used to assemble, update and curate this data set long-term [@Backman2011-uw; @Cao2008-zo]. Most small molecules will be identified by integrating several large-scale community data sources such as data from drug databases (e.g. Drugbank), bioassay databases (e.g. PubChem Bioassay, ChEMBL), literature, drug-related gene expression fingerprints (e.g. LINCS), genetic (e.g. GWAS) and phenotype resources. This will also include nearest neighbors of LADs sharing with them structural, physicochemical or biological properties.

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Getting Started

The R software for running longevityTools can be downloaded from CRAN. The longevityTools package can be installed from the R console using the following biocLite install command.

source("http://bioconductor.org/biocLite.R") # Sources the biocLite.R installation script 
biocLite("tgirke/longevityTools", build_vignettes=FALSE) # Installs package from GitHub

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library("longevityTools") 
library("ChemmineR")

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Load database

mypath <- system.file("extdata", "longevitydrugs.sdf", package="longevityTools")
sdfset <- read.SDFset(mypath)
data(sdfsample)
sdfsample

## An instance of "SDFset" with 100 molecules

plot(sdfsample[1:4], print=FALSE)

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Funding

This project is funded by NIH grant U24AG051129 awarded by the National Intitute on Aging (NIA).

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Version information

sessionInfo()

## R version 3.2.2 (2015-08-14)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: CentOS Linux 7 (Core)
## 
## locale:
## [1] C
## 
## attached base packages:
## [1] stats     graphics  utils     datasets  grDevices methods   base     
## 
## other attached packages:
## [1] ChemmineR_2.22.3     ggplot2_2.0.0        longevityTools_1.0.6 BiocStyle_1.8.0     
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_0.12.3      codetools_0.2-14 digest_0.6.9     bitops_1.0-6     plyr_1.8.3      
##  [6] grid_3.2.2       DBI_0.3.1        gtable_0.1.2     formatR_1.2.1    magrittr_1.5    
## [11] evaluate_0.8     scales_0.3.0     stringi_1.0-1    rmarkdown_0.9.2  rjson_0.2.15    
## [16] tools_3.2.2      stringr_1.0.0    RCurl_1.95-4.7   munsell_0.4.3    yaml_2.1.13     
## [21] colorspace_1.2-6 htmltools_0.3    knitr_1.12.3

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