kmeRs2: k-Mers Similarity Score Matrix

This is an updated version of kmeRs with native R support for both DNA and amino acid k-mers, along with faster package loading times, performance and the ability to plot similarity score heatmap in R. kmeRs2 contains tools to calculate Needleman-Wunsch or Smith-Waterman similarity score matrices with based on user's choice of PAM or BLOSUM substitution methods.

Installation

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("Biostrings")
# install.packages("devtools")
devtools::install_github("jlincbio/kmeRs2")

Alternatively, use the release tarball and install via the command line:

R CMD INSTALL <kmeRs2-1.0.0.tar.gz>

R Dependencies

• Biostrings
• RColorBrewer (suggested)

Citation

Please cite the original kmeRs by R. Urniaz if you use kmeRs2:

Urniaz R., "kmeRs: an R package for k-mers similarity score calculations", Version 1.0, 2018. URL: cran.r-project.org/package=kmeRs.

Additionally, kmeRs_generate_kmers and kmeRs_twoSeqSim were sourced from tcR and rDNAse, respectively.