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Dependencies/Requirements

Some functions of this package require Bioconductor libraries. These functions should install automatically with the package. Anyway, install Bioconductor repository is recommended.

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

The possibile required packages are: Biostrings, biomaRt, GO.db, rtracklayer. To install them directly you need to have previously installed BiocManager and then:

BiocManager::install(c("Biostrings", "biomaRt", "GO.db", "rtracklayer"))

deepTools

Certain functions of this package require that deeptools is installed on your system. For more information see the deepTools installation page.

  • Installation via conda: conda install -c bioconda deeptools
  • Command line installation using pip: pip install deeptools, All python requirements should be automatically installed.

bedTools

Certain functions of this package require that bedtools is installed on your system. For more information see the bedTools installation page.

  • Installation via conda: conda install -c bioconda bedtools
  • Command line installation:
    • Fedora/Centos: yum install BEDTools
    • Debian/Ubuntu: apt-get install bedtools
    • Homebrew (MacOS): brew tap homebrew/science; brew install bedtools
    • MacPorts: port install bedtools

Installation

# Install devtools from CRAN
install.packages("devtools")

# Or the development version from GitHub:
## install.packages("devtools")
## devtools::install_github("r-lib/devtools")

# Install the Rseb package
devtools::install_github("sebastian-gregoricchio/Rseb")

Documentation

With the package a PDF manual is available.

Contact

For any suggestion, bug fixing, commentary please contact Sebastian Gregoricchio at sebastian.gregoricchio@gmail.com.

License

This package is under a GNU General Public License (version 3).