README.md

In wind22zhu/rDNAse: R package for generating various numerical representation schemes of DNA sequences.

rDNAse

Comprehensive toolkit for generating various numerical representation schemes of DNA sequence. The descriptors included in the rDNAse package are extensively utilized in bioinformatics and chemogenomics.

Package Description

Commonly used descriptors

• Nucleic acid composition

  • Basic kmer
  • Reverse compliment kmer
  • Increment of diversity

• Autocorrelation

  • Dinucleotide-based auto covariance
  • Dinucleotide-based cross covariance
  • Dinucleotide-based auto-cross covariance
  • Trinucleotide-based auto covariance
  • Trinucleotide-based cross covariance
  • Trinucleotide-based auto-cross covariance

• Nucleic acid composition

  • Pseudo dinucleotide composition
  • Pseudo k-tupler nucleotide composition

Similarity Computation

Local and global pairwise sequence alignment for DNA sequences:

• Between two DNA sequences
• Parallelized pairwise similarity calculation with a list of DNA sequences

GO semantic similarity measures:

• Between two groups of GO terms / two Entrez Gene IDs
• Parallelized pairwise similarity calculation with a list of GO terms / Entrez Gene IDs

Links

• CRAN: https://cran.r-project.org/package=rDNAse
• GitHub: https://github.com/wind22zhu/rDNAse
• Bug report: https://github.com/wind22zhu/rDNAse/issues

wind22zhu/rDNAse documentation built on May 4, 2019, 6:31 a.m.