Package: DESNP 0.1.0

Sayanti Guha Majumdar

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.

Authors:Sayanti Guha Majumdar [aut, cre], Saima Bano [aut], Nandita Banerjee [aut], Rahul Kumar Tiwari [aut], Dipro Sinha [aut], Subham Ghosh [aut], Sanjeev Kumar [aut]

DESNP_0.1.0.tar.gz
DESNP_0.1.0.tar.gz(r-4.7-any)DESNP_0.1.0.tar.gz(r-4.6-any)
DESNP_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
DESNP/json (API)

# Install 'DESNP' in R:
install.packages('DESNP', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.00 score 521 downloads 4 exports 58 dependencies

Last updated from:056b8fae83. Checks:4 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK189
source / vignettesOK188
linux-release-x86_64OK196
wasm-releaseOK114

Exports:DeltaSNPindexDeltaSNPWindowmanhattan_plotSNPindex

Dependencies:apeaskpassBiocGenericscliclustercpp11curldigestdplyrfarvergenericsGenomeInfoDbGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmemusemgcvmimenlmeopensslpermutepillarpinfsc50pkgconfigpurrrR6RColorBrewerRcpprlangS4VectorsS7scalesSeqinfostringistringrsystibbletidyrtidyselectUCSC.utilsutf8vcfRvctrsveganVGAMviridisLitewithr