rSWeeP lite

The rSWeeP package is an R implementation of the SWeeP method. The main function of this package is to provide a vector representation of biological sequences (nucleotides or amino acids), and thus favor alignment-free phylogenetic studies. Each sequence provided is represented by a compact numerical vector which is easier to analyze. The method is based on k-mers counting and random projection of high-dimensional vectors into low-dimensional vectors. In addition, the package allows general dimensionality reduction of RNAseq data and generic matrices.

rSWeeP

rSWeeP: Functions to creation of low dimensional comparative matrices of Amino Acid Sequence occurrences

The SWeeP method was developed to favor the analizes between amino acids sequences and to assist alignment free phylogenetic studies. This method is based on the concept of sparse words, which is applied in the scan of biological sequences and its the conversion in a matrix of ocurrences. Aiming the generation of low dimensional matrices of Amino Acid Sequence occurrences.