jirihon / pqsfinder-legacy

Detect the positions of intramolecular G4-quadruplexes. This repository was used prior to Bioconductor submission.

pqsfinder package

This package provides functions for identification of potential intramolecular quadruplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular G4-quadruplex in a much larger sequence.

How to Install

Download the latest develompment version of R:

wget https://stat.ethz.ch/R/daily/R-devel.tar.gz

Unpack:

tar -xzf R-devel.tar.gz

Configure with --enable-R-shlib option in case you want to run the newest R inside RStudio. It is possible, you will be required to install additional libraries. The corresponding package names are usually in the form libXXX-dev, where XXX is the name of the library.

cd R-devel
./configure --enable-R-shlib=yes

Only compile. There is no reason to run make install as the resulting binary can be run directly from the compilation folder without messing up your system.

make

Run:

./bin/R

Install Bioconductor and pqsfinder package dependencies:

source("https://bioconductor.org/biocLite.R")
biocLite()

biocLite(c("Rcpp", "GenomicRanges", "Biostrings", "flowCore", "devtools"))

Install pqsfinder package directly from GitHub:

library("devtools")
install_github("jirihon/pqsfinder")