DESNP: Differentially Expressed Single Nucleotide Polymorphism
Provides a framework for the identification and analysis of Differentially Expressed Single Nucleotide Polymorphisms (deSNPs) using high-throughput sequencing data. It enables users to import SNP count data from variant files, perform allele-specific read count extraction, and statistically detect SNPs showing significant differences in allele expression between biological conditions or sample groups. This package contains tools for calculating SNP-index and Delta SNP-index from VCF-derived allele depth data with statistical testing and filtering, including sliding-window analysis of genomic regions.
| Version: |
0.1.0 |
| Depends: |
R (≥ 4.1.0) |
| Imports: |
vcfR, dplyr, tidyr, magrittr, tidyselect, VGAM, stats, utils, GenomicRanges, IRanges, S4Vectors, GenomeInfoDb, tools, ggplot2 |
| Published: |
2026-03-19 |
| DOI: |
10.32614/CRAN.package.DESNP (may not be active yet) |
| Author: |
Sayanti Guha Majumdar [aut, cre],
Saima Bano [aut],
Nandita Banerjee [aut],
Rahul Kumar Tiwari [aut],
Dipro Sinha [aut],
Subham Ghosh [aut],
Sanjeev Kumar [aut] |
| Maintainer: |
Sayanti Guha Majumdar <sayanti23gm at gmail.com> |
| License: |
GPL-3 |
| NeedsCompilation: |
no |
| CRAN checks: |
DESNP results |
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