Rsearch

1.1.0

Processing and Analyzing Amplicon Sequence Data

0packages depend

1.6Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Cassandra StamsaasFirst published 2025-10-262 releasesCRAN page ↗GitHub ↗

Processing and analysis of targeted sequencing data. The package provides a user-friendly interface for core 'VSEARCH' (Rognes et al. (2016), doi:10.7717/peerj.2584) functions, in addition to tools for visualization and parameter tuning.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

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

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

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("CassandraHjo/Rsearch")

Development version from CassandraHjo/Rsearch. Installs pak first if it is not already available.

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-rsearch

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: 2.3 min · r-release-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-10
12 OK · 0 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE

Documentation

READMEYes · 1,120 wordsVignettesNopkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 24%
Documented parameters: 99%
Return-value docs: 100%
References docs: 69%

Downloads

1.6K

CRAN downloads in the past year

Rank #19,288 · ~4/day · ~131/mo

Releases R versions

Daily download trend is not available in this view yet.

17530 days

62290 days

1.6K1 year

Compare downloads with other packages →

Also on48 r2u

Repository

GitHub ↗ cassandrahjo/rsearch

1Stars

1Forks

0Open issues

0Open PRs

1Releases

570Commits

4Contributors

16sampliconbioinformaticsfastafastqvsearchclusteringdenoising

License GPL-3.0 · 570 commits · Last activity 2026-07-20

Issues over time

2026-07-14 · 02026-07-20 · 1

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/cassandrahjo/rsearch on 2026-07-19.

Reproducibility and dev environment (1)

renv

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1

Imports (14)

ape cowplot dplyr ggExtra (>= 0.10.1)ggplot2 microseq phyloseq (>= 1.50.0)RColorBrewer readrstatsstringr tibble tidyr tidyselect

LinkingTo (0)

none

Suggests (3)

rmarkdown testthat withr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 7,678 (68%)Rd 3,673 (32%)

Code characteristics

Cyclomatic complexity: 12.0 median / 99 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

40 31 exported

Complexity

16.7 avg / 99 max

Call network

40 nodes / 53 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (4)

Maintainer (1)

Cassandra Stamsaas

Maintainer, Author

Authors (4)

Maintainer, Author

Author

Author

Author

Package Timeline

2 releases. Pick two to compare their code metrics. R releases are shown for context.

1.1.0Latest
2026-07-20 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.0.0
2026-03-10
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-10-26
Total releases: 2 / 1 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.1
Download size: 412 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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