R Observatory: Metrics for CSeQTL version 1.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CSeQTL

1.0.1Package record

Cell Type-Specific Expression Quantitative Trait Loci Mapping

0packages depend

3.5Kdownloads / year

–test coverage

10/13flavors OK

Overview

About

Maintained by Paul LittleCRAN page ↗GitHub ↗

Perform bulk and cell type-specific expression quantitative trait loci mapping with our novel method (Little et al. (2023) doi:10.1038/s41467-023-38795-w).

Install

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

install.packages("CSeQTL", 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("pllittle/cseqtl")

Development version from pllittle/cseqtl. 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-cseqtl

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-CSeQTL

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-CSeQTL

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

3WARNING10OK

Check messages

WARNINGwhether package can be installedr-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-release-macos-x86_64

r-oldrel-macos-arm64

Found the following significant warnings:
  all_functions.cpp:1382:11: warning: explicitly assigning value of variable of type 'arma::vec' (aka 'Col<double>') to itself [-Wself-assign-overloaded]
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.5/CSeQTL.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
* used SDK: ‘MacOSX11.3.1.sdk’

r-oldrel-macos-x86_64

Found the following significant warnings:
  all_functions.cpp:1382:11: warning: explicitly assigning value of variable of type 'arma::vec' (aka 'Col<double>') to itself [-Wself-assign-overloaded]
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.5/CSeQTL.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
* used SDK: ‘NA’

r-release-macos-x86_64

Found the following significant warnings:
  all_functions.cpp:1382:11: warning: explicitly assigning value of variable of type 'arma::vec' (aka 'Col<double>') to itself [-Wself-assign-overloaded]
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.6/CSeQTL.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
* used SDK: ‘MacOSX11.3.1.sdk’

CRAN check page ↗

Slowest check: 7.0 min · r-oldrel-windows-x86_64

Status changes

WARNING10 OK, 3 WARNING2026-06-09
ERROR9 OK, 3 WARNING, 1 ERROR2026-06-08
WARNING4 OK, 3 WARNING2026-04-25
ERROR7 OK, 4 WARNING, 3 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.1

README· In the repository, left out of the releaseVignettesYes · 1 · dynamicNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 10
Examples that run: no examples
Exported functions with examples: 0%
Documented parameters: 98%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

test

How these are measured

Downloads

3.5K

CRAN downloads in the past year

Rank #10,377 · ~9/day · ~288/mo

Releases R versions

Daily download trend is not available in this view yet.

33230 days

98190 days

3.5K1 year

Compare downloads with other packages →

Also on378 r2u15 autocran

How downloads are counted

Repository

pllittle/cseqtl ↗Account: pllittle

4Stars

1Forks

0Open issues

0Open PRs

2Releases

30Commits

1Commit identities

gene-expressionrna-seqgenomicscell-typeseqtl-mappingphased-genotypesenrichment-analysis

License file reads as GPL-3.0 · 30 commits · Last activity 2026-05-04 · 0% stars, 30d

Responsiveness

not measured

Stars over time

2024-02-18 · 32026-08-07 · 4

How these are measured

PracticesBeta

Checks run against github.com/pllittle/cseqtl on 2026-10-18.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing CSeQTL adds 128 packages (60 with compiled code, 94 MB of source tarballs). Heaviest: stringi 11 MB, TH.data 8.2 MB, ggplot2 6.0 MB.

Depends (1)

R >= 3.5.0

Imports (10)

Rcpp smarter ggplot2 multcomp emdbook MatrixEQTL data.table HelpersMG R.utilsmethods

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (2)

rmarkdown knitr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (1)

Paul Little

Author, Maintainer since 1.0.0 (2025)

Releases (2)

Pick two releases to compare their code metrics.

unarchivedReturned to CRAN
2026-04-24
1.0.1Latest
record
2026-04-24 · current release · diff ↗ ·
removed 1 export
prep_gene_info
R
R 4.6.0 released · 2026-04-24
archivedRemoved from CRAN
2026-04-13
issues were not corrected despite reminders
R
R 4.5.0 released · 2025-04-11
1.0.0
record
2025-03-06
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2025-03-06
Total releases: 2 / 1 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.5.0
Download size: 1.0 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("CSeQTL")

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

It points to 10.1038/s41467-023-38795-w.

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 CSeQTL version 1.0.1 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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