R Observatory: Metrics for DESNP version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

DESNP

0.1.0Package record

Differentially Expressed Single Nucleotide Polymorphism

0packages depend

3Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Sayanti Guha MajumdarCRAN 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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 4.2 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK5 OK2026-03-20

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.0

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 4
Examples that run: 100%4 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 75%

How these are measured

Downloads

3K

CRAN downloads in the past year

Rank #11,060 · ~8/day · ~253/mo

Releases R versions

Daily download trend is not available in this view yet.

33830 days

95690 days

3K1 year

Compare downloads with other packages →

Also on48 r2u

How downloads are counted

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing DESNP adds 38 packages (22 with compiled code, 40 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, pinfsc50 3.3 MB. 4 more not on CRAN are not measured.

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.

How these are counted

Code & Tests

Datasets

People & History

People (7)

Sayanti Guha Majumdar

Author, Maintainer since 0.1.0 (2026)

Author

Author

Author

Author

Author

Author

Releases (1)

R
R 4.6.0 released · 2026-04-24
0.1.0Latest
record
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

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 package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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