Reputils

The Reputils R package is a beta development version to facilitate analysis of transposable elements.

Features include:

  • Import of various TE coodinate formats
  • Curation of TE intervals
  • Mapping benchmarking

More details on the usage of Reputils is available in the package vignette.

Installation

# Install BiocManager (in case you haven't already)
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# Install Reputils
install.packages('Reputils', repos = 'tanaylab.bitbucket.io/repo')

Note: Reputils requires R version 3.5 or higher. The package was tested on linux and macbook machines, but is currently not compatible on Windows. A typical application will require at least 4 GB RAM, but heavier use cases (e.g. large BAM files) may require significantly more. For improved speed performance, we recommend a multi-CPU/core workstation.