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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 |
| 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 |
| Reference manual: | DESNP.html , DESNP.pdf |
| Package source: | DESNP_0.1.0.tar.gz |
| Windows binaries: | r-devel: DESNP_0.1.0.zip, r-release: DESNP_0.1.0.zip, r-oldrel: DESNP_0.1.0.zip |
| macOS binaries: | r-release (arm64): DESNP_0.1.0.tgz, r-oldrel (arm64): DESNP_0.1.0.tgz, r-release (x86_64): DESNP_0.1.0.tgz, r-oldrel (x86_64): DESNP_0.1.0.tgz |
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These binaries (installable software) and packages are in development.
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