Install From Github

install.packages("devtools")

install Bioconductor packages

source("http://bioconductor.org/biocLite.R")
BiocInstaller::biocLite(c('GenomeInfoDb',
                        'IRanges',
                        'DESeq2',
                        'GenomicAlignments',
                        'SummarizedExperiment',
                        'GenomicRanges',
                        'Rsamtools',
                        'org.Hs.eg.db',
                        'clusterProfiler',
                        'ensembldb', 
                        'EnsDb.Hsapiens.v75',
                        'GO.db'))

install the package

devtools::install_github("mathelab/ALTRE")

When installing on Linux, if you get an rJava package installation error. Please run the following two lines in the console:

sudo apt-get install openjdk-7-*
sudo R CMD javareconf

On Windows, if you get an installation error then first run the following lines of code in as well:

install.packages(c("htmltools","httpuv","evaluate","markdown"))

When installing on OSC cluster, if you get an installation error then first run the following lines of code in your console prior to trying to install:

sudo R CMD javareconf -e
export JAVA_CPPFLAGS='-O2'
module load gnu/5.2.0
module load R/3.3.1

Installation Walk-through Animation

To Run

To launch the Shiny app inside R, run

library(ALTRE)
runShinyApp()

Shiny App Preview

Vignette

A vignette (which provides an overview of the package via step-by-step guide through an example dataset) is here: https://mathelab.github.io/ALTRE/vignette.html

Data

A restricted subset of the data with one chromosome (i.e. chromosome 21) can be found on this page. The corresponding CSV file for input into ALTRE can be downloaded here. Be sure to modify the datapath column of the CSV file so that the appropriate full path of the data files on your local machine is included.

To download the entire data, please use a file download manager to download the files from the links listed below.

Alignment (in BAM format) files:

A549:

https://www.encodeproject.org/files/ENCFF001CLE/@@download/ENCFF001CLE.bam

https://www.encodeproject.org/files/ENCFF001CLJ/@@download/ENCFF001CLJ.bam

SAEC:

https://www.encodeproject.org/files/ENCFF001EFI/@@download/ENCFF001EFI.bam

https://www.encodeproject.org/files/ENCFF001EFN/@@download/ENCFF001EFN.bam

Peak/hotspot (in BED format) files:

A549:

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseA549HotspotsRep1.broadPeak.gz

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseA549HotspotsRep2.broadPeak.gz

SAEC:

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseSaecHotspotsRep1.broadPeak.gz

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwDnase/wgEncodeUwDnaseSaecHotspotsRep2.broadPeak.gz

Blacklisted genomic regions for functional genomics analysis

https://sites.google.com/site/anshulkundaje/projects/blacklists