diffSeqPatterns

diffSeqPatterns is an R package to comprehensively analyse differential sequence patterns between any two groups of peptides. The diffSeqPatterns provides functionality to analyse and visualize differential patterns in:

• Position-specific amino acid usage
• N-grams: contiguous sequences of n-amino acids
• Position-specific k-mer motifs: contiguous or non-contiguous sequences of k amino acids
• Inter-sequence distance or alignment score: Pairwise distance (e.g. Hamming, levenshtein, Jaccard distance) or global/local alignment using substitution matrix of interest (e.g. BLOSUM62).

Analysis and visualization tools in diffSeqPatterns can be applied to identify conserved patterns in any peptides, such as cancer neoepitopes, SARS-CoV-2 epitopes or antimicrobial peptides.

Installing

Install diffSeqPatterns from github:

library(devtools)
install_github("ChloeHJ/diffSeqPatterns", build_vignettes = TRUE)

Install diffSeqPatterns from CRAN:

library(diffSeqPatterns)

Exploring the package

Browse the vignette:

browseVignettes('diffSeqPatterns')