R Observatory: Metrics for noisyr version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

noisyr

1.0.0Package record

Noise Quantification in High Throughput Sequencing Output

0packages depend

2.8Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Ilias MoutsopoulosCRAN page ↗GitHub ↗Issues ↗

Quantifies and removes technical noise from high-throughput sequencing data. Two approaches are used, one based on the count matrix, and one using the alignment BAM files directly. Contains several options for every step of the process, as well as tools to quality check and assess the stability of output.

Install

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

install.packages("noisyr", 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("Core-Bioinformatics/noisyR")

Development version from Core-Bioinformatics/noisyR. 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-noisyr

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: 4.0 min · r-release-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.0

READMEYes · 703 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileNo

Help pages: 18
Examples that run: 100%18 run in a plain check
Exported functions with examples: 100%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 0%

Vignettes (1)

noisyR count matrix approach workflow

How these are measured

Downloads

2.8K

CRAN downloads in the past year

Rank #15,078 · ~8/day · ~233/mo

Releases R versions

Daily download trend is not available in this view yet.

29330 days

80990 days

2.8K1 year

Compare downloads with other packages →

Also on109 r2u186 bioconda

How downloads are counted

Repository

core-bioinformatics/noisyr ↗Organization: Core-Bioinformatics

10Stars

0Forks

0Open issues

0Open PRs

2Releases

32Commits

2Commit identities

32 commits · Last activity 2021-10-01 · 0% stars, 30d · Default branch at 1.1.0, ahead of CRAN 1.0.0 (checked 2026-10-21)

Responsiveness

not measured

Stars over time

2025-09-24 · 102026-07-07 · 10

How these are measured

PracticesBeta

3 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/core-bioinformatics/noisyr on 2026-10-21.

Docs source (2)

pkgdown

GitHub Pages site last deployed 2021-10-01

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing noisyr adds 32 packages (15 with compiled code, 19 MB of source tarballs). Heaviest: ggplot2 6.0 MB, Rcpp 1.8 MB, isoband 1.5 MB. 4 more not on CRAN are not measured.

Depends (1)

R >= 3.1.2

Imports (13)

utilsgrDevicestibble dplyr magrittr ggplot2 preprocessCore IRanges GenomicRanges Rsamtools philentropy doParallel foreach

LinkingTo (0)

none

Suggests (4)

testthat roxygen2 knitr rmarkdown

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 (4)

Ilias Moutsopoulos

Author, Maintainer since 0.1.0 (2021)

Irina Mohorianu

Author, Contributor

Hajk-Georg Drost

Contributor

Elze Lauzikaite

Contributor

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.0.0Latest
record
2021-04-16 · current release · diff ↗
0.1.0
record
2021-01-06
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-01-06
Total releases: 2 / 5 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.1.2
Download size: 3.0 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("noisyr")

Format

Moutsopoulos, I., Drost, H., Lauzikaite, E., & Mohorianu, I. (2021). noisyr: Noise Quantification in High Throughput Sequencing Output (Version 1.0.0) [Computer software]. https://doi.org/10.32614/CRAN.package.noisyr

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 noisyr version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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