BiocStyle::markdown() options(width=100, max.print=1000) knitr::opts_chunk$set( eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")), cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE")))
suppressPackageStartupMessages({ library(longevityTools) library(ggplot2) })
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.
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
library("longevityTools") library("ChemmineR")
mypath <- system.file("extdata", "longevitydrugs.sdf", package="longevityTools") sdfset <- read.SDFset(mypath) data(sdfsample) sdfsample plot(sdfsample[1:4], print=FALSE)
This project is funded by NIH grant U24AG051129 awarded by the National Intitute on Aging (NIA).
sessionInfo()
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