README.md

In svenbioinf/OGRE: Calculate, visualize and analyse overlap between genomic regions

OGRE - Overlapping annotated Genomic REgions Calculate, visualize and analyse overlap between genomic regions

The OGRE package calculates overlap between user defined genomic region datasets. Any regions can be supplied i.e. genes, SNPs, or reads from sequencing experiments. Key numbers help analyse the extend of overlaps which can also be visualized at a genomic level.

Click here to download OGRE's Vignette as PDF

https://user-images.githubusercontent.com/68910402/203071312-ff92a42d-05c6-4c83-9905-f47e477305e9.mp4

Installation via GitHub

For installing OGRE by GitHub use the install_github() function.

if(!requireNamespace("remotes", quietly = TRUE)){
    install.packages("remotes")
}
remotes::install_github("svenbioinf/OGRE",build_vignettes = TRUE)

OGRE depends on the following packages:

• IRanges
• GenomicRanges
• S4Vectors
• methods
• data.table
• assertthat
• ggplot2
• Gviz
• AnnotationHub
• shiny
• shinyFiles
• DT
• rtracklayer
• shinydashboard
• shinyBS
• tidyr
• GenomeInfoDb

if not automatically installed, those can be installed with:

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install(c(
"IRanges",
"GenomicRanges",
"S4Vectors",
"methods",
"data.table",
"assertthat",
"ggplot2",
"IRanges",
"Gviz",
"AnnotationHub",
"shiny",
"shinyFiles",
"DT",
"rtracklayer",
"shinydashboard",
"shinyBS",
"tidyr",
"GenomeInfoDb"
))

The OGRE package itself can then be loaded with the following commands:

library(OGRE) # load package
vignette("OGRE") #some information on how to use the package

Installation via Bioconductor

(Once OGRE is available on Bioconductor, if not- use devel version below.)

Start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("OGRE")
library(OGRE)    # load package
vignette("OGRE") # some information on how to use the package

Installation via Bioconductor (develop version)

Start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("OGRE",version = "devel")
library(OGRE)    # load package
vignette("OGRE") # some information on how to use the package

Installation via docker

Using docker you can easily install OGRE with the latest R and RStudio software and all required packages already included. For this to work, your local computer needs to have docker installed.

sudo apt install docker.io #on linux via console

For windows just follow instructions on: docker.com. You can then pull OGRE's docker file from dockerHub and install by copying the following to your shell (console).

sudo docker pull svenbioinf/ogre:1 #on linux shell
sudo docker run -e PASSWORD=ogre -p 8787:8787 svenbioinf/ogre:1 #on linux shell

docker pull svenbioinf/ogre:1 #on windows console
docker run -e PASSWORD=ogre -p 8787:8787 svenbioinf/ogre:1 #on windows console

After installation, open RStudio using your favorite browser on http://localhost:8787 username=rstudio, password=ogre. You can then load OGRE, browse the vignette or run the GUI with

library("OGRE")
vignette("OGRE")
SHREC()

Contact

This software was developed by Sven Berres svenbioinf(AT)gmail.com

svenbioinf/OGRE documentation built on Jan. 30, 2023, 10:55 p.m.