# ALTRE R Package
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## What is ALTRE?

ALTRE enables easy comparison of chromatin accessibility between two samples (each sample must have at least two replicates). Chromatin accessibility information is obtained through assays such as ATAC-seq and Dnase-seq. By default, ALTRE works on the hg19 human genome. However, the __new update (01/25/2017)__ enables ALTRE to easily take on other human builds or other organisms entirely. However, it is up to users to provide their own file of gene transcription start sites to supply to the getTSS function. This file can be created from a gtf file. 

See here for more information about creating the required file: 
https://github.com/Mathelab/ALTREsampledata/tree/master/gtfManipulation

Additional information also available in the documentation for the *getTSS()* function.

Installation instructions below or if you want to see an example of how ALTRE works without installation browse the vignette: https://mathelab.github.io/ALTRE/vignette.html


## Contact Us
If you encounter any problems running on the software, or find installation problems or bugs, please start an issue on the Issues tab or email Ewy.Mathe@osumc.edu directly. Thanks! 

## ALTRE prerequisites 

ALTRE is a package for the R statisical programming language. ALTRE can be run on R version >=3.2.0, but for quickest installation, R >= 3.3.0 is recommended.

Download (or upgrade) R here: https://cloud.r-project.org/

RStudio (an interface to R than can make R easier to use) can be download here (not required): https://www.rstudio.com/products/rstudio/download3/

## Installation From Github


To install ALTRE, run the following code in the R terminal

```{R}
# First, install the Bioconductor packages (dependencies) with these two lines           
source("http://bioconductor.org/biocLite.R")
BiocInstaller::biocLite(c('org.Hs.eg.db', 'EnsDb.Hsapiens.v75', 'GO.db'))
# Second, install the devtools package for installing ALTRE from GitHub
install.packages("devtools") 
# Third, install the ALTRE package 
devtools::install_github("mathelab/ALTRE")
```
If you are installing on a Linux or MacOS operating system it is highly recommended that you install one additional package:

```{R}
BiocInstaller::biocLite(c('Rsubread'))
```
This package will enable you to run one step of the pipeline significantly faster than Windows users. The extra package is not available for Windows (attempting to install it will produce an error). 

If you encounter an error when runing the above lines, please do the following:

### On Linux and MacOS


When installing on Linux, installation might fail if the XML package cannot be installed. Installation failure  can be fixed by installing the libxml2, an XML C parser for Linux. Also to install the devtools R library, you also need to install several system dependencies. 

On Ubuntu this can be done by running the following line in the terminal:

```{R}
sudo apt-get install libxml2-dev libssl-dev libcurl4-openssl-dev gfortran
```
On Mac OS, the same dependecies can installed using the *brew* command. 

On Red-hat Enterprise Linux or CentOS it is the following:

```{R}
sudo yum install libcurl-devel openssl-devel libxml2-devel
```


### On Windows


if you get an installation error then first run the following lines of code in the R console:

```{R}
install.packages(c("htmltools","httpuv","evaluate","markdown"))
```

### Installation Walk-through Screencast

![](inst/img/ALTREinstall.gif)


## Running and Launching the Shiny App

To launch the Shiny app inside R, run

```{R}
library(ALTRE)
runShinyApp()
```

### Shiny App How to Run Screencast

![](inst/img/ALTRErun.gif)


### Shiny App Preview


![](inst/img/ALTREprev.gif)

##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

When using your own data, be sure that extraneous annotations (e.g. chrN_random sequences) are removed from your peak files and annotation files.  You may have to remove them from your alignment (bam) files as well since the software will not recognize these as valid entries.

## Sample Data

A restricted subset of the data with one chromosome (i.e. chromosome 21) can be found on this [page](http://mathelab.github.io/ALTREsampledata/). The corresponding CSV file for input into ALTRE can be downloaded [here](https://raw.githubusercontent.com/mathelab/ALTREsampledata/master/DNaseEncodeExample.csv). Be sure that the CSV file and the data files are in the same folder when running analysis with ALTRE.

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

### Highcharts

All plots from this package use Highcharts:
Highcharts (www.highcharts.com) is a Highsoft software product which is
not free for commercial and Governmental use.