SeqCountGenome

Bioconductor compliant package for counting sequences occurrences in arbitrary subsets of the genome, realized for the Scientific Programming course of the Bioinformatics for Computational Genomics MSc.

Installation

For installing this package in R, the devtools::install_github() command is required:

if (!require("devtools")) {install.packages("devtools")}
devtools::install_github("dacolombo/SeqCountGenome")

Once installed, the package can be loaded with:

library(SeqCountGenome)

Usage

For information about how to use the function contained in this package, refer to the manual in this github repository: SeqCountGenome-manual.pdf.

Otherwhise, after installing the package consult the vignette using this command in an R session:

utils::browseVignettes("SeqCountGenome")

Dependencies

This package main dependencies are the following Bioconductor packages: BSgenome, Biostrings, GenomeInfoDb and GenomicRanges