R Observatory: Metrics for DESNP version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

DESNP

0.1.0

Differentially Expressed Single Nucleotide Polymorphism

0packages depend

2.3Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Sayanti Guha MajumdarFirst published 2026-03-191 releasesCRAN page ↗

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.

Install

R (CRAN)Ubuntu (r2u)

install.packages("DESNP", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-desnp

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

13OK

Slowest check: 4.5 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

14

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-20
5 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 75%

Downloads

2.3K

CRAN downloads in the past year

Rank #8,683 · ~6/day · ~188/mo

Releases R versions

Daily download trend is not available in this view yet.

20730 days

1.1K90 days

2.3K1 year

Compare downloads with other packages →

Also on42 r2u

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (14)

vcfR dplyr tidyr magrittr tidyselect VGAMstatsutilsGenomicRanges IRanges S4Vectors GenomeInfoDbtoolsggplot2

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (7)

Maintainer (1)

Sayanti Guha Majumdar

Author, Maintainer

Authors (7)

Sayanti Guha Majumdar

Author, Maintainer

Author

Author

Author

Author

Author

Author

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.0Latest
2026-03-19 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-03-19
Total releases: 1 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1.0
Download size: 41 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("DESNP")

Format

Guha Majumdar, S., Banerjee, N., Bano, S., Ghosh, S., Kumar, S., Sinha, D., & Tiwari, R. K. (2026). DESNP: Differentially Expressed Single Nucleotide Polymorphism (Version 0.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.DESNP

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for DESNP version 0.1.0 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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