R Observatory: Metrics for BootstrapQTL version 1.0.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

BootstrapQTL

1.0.5Package record

Bootstrap cis-QTL Method that Corrects for the Winner's Curse

0packages depend

3.2Kdownloads / year

66.1%test coverage

11/13flavors OK

Overview

About

Maintained by Scott RitchieCRAN page ↗GitHub ↗Issues ↗

Identifies genome-related molecular traits with significant evidence of genetic regulation and performs a bootstrap procedure to correct estimated effect sizes for over-estimation present in cis-QTL mapping studies (The "Winner's Curse"), described in Huang QQ *et al.* 2018 <doi: 10.1093/nar/gky780>.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("BootstrapQTL", 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("sritchie73/bootstrapQTL")

Development version from sritchie73/bootstrapQTL. 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-bootstrapqtl

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

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-BootstrapQTL

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-BootstrapQTL

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Scott Ritchie <sritchie73@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Qin", "Qin"),
                      family = "Huang",
                      role = "aut"),
               person(given = "Scott",
                      family = "Ritchie",
                      role = c("aut", "cre"),
                      email = "sritchie73@gmail.com"))
as necessary.

CRAN check page ↗

Slowest check: 2.5 min · r-release-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.5

READMEYes · 288 wordsVignettesNoNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 1
Examples that run: 100%1 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

3.2K

CRAN downloads in the past year

Rank #13,568 · ~9/day · ~266/mo

Releases R versions

Daily download trend is not available in this view yet.

34730 days

84690 days

3.2K1 year

Compare downloads with other packages →

Also on86 r2u24 autocran

How downloads are counted

Repository

sritchie73/bootstrapqtl ↗Account: sritchie73

6Stars

1Forks

1Open issues

0Open PRs

0Releases

85Commits

1Commit identities

85 commits · Last activity 2021-05-11

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 0
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2021-02-17 · 62026-07-07 · 6

How these are measured

PracticesBeta

Checks run against github.com/sritchie73/bootstrapqtl on 2026-10-11.

No development-tooling practices detected in the upstream repository.

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing BootstrapQTL adds 4 packages (1 with compiled code, 6.1 MB of source tarballs). Heaviest: data.table 5.7 MB, iterators 293 KB, foreach 88 KB.

Depends (1)

MatrixEQTL

Imports (2)

foreach data.table

LinkingTo (0)

none

Suggests (4)

doMC doParallel qvalue testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (from the free-text Author field) (2)

Scott Ritchie

Author, Maintainer since 1.0.2 (2018)

Qin Qin Huang

Author

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
1.0.5Latest
record
2021-05-12 · current release · diff ↗
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
1.0.2
record
2018-09-22
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-09-22
Total releases: 2 / 8 yrs
License: GPL-2 OSI
Download size: 17 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("BootstrapQTL")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1093/nar/gky780.

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 BootstrapQTL version 1.0.5 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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