CSeQTL

1.0.1

Cell Type-Specific Expression Quantitative Trait Loci Mapping

0packages depend

3.2Kdownloads / year

–test coverage

10/13checks pass

Overview

About

Maintained by Paul LittleFirst published 2025-03-062 releasesCRAN 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.

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).

Health

CRAN checks

3WARNING10OK

Failing flavors

WARNING r-oldrel-macos-arm64
WARNING r-oldrel-macos-x86_64
WARNING r-release-macos-x86_64

Slowest check: 7.7 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

WARNING2026-06-09
10 OK · 0 NOTE · 3 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
9 OK · 0 NOTE · 3 WARNING · 1 ERROR · 0 FAILURE
WARNING2026-04-25
4 OK · 0 NOTE · 3 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-10
7 OK · 0 NOTE · 4 WARNING · 3 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: not tracked
Documented parameters: 98%
Return-value docs: 100%
References docs: 0%

Downloads

3.2K

CRAN downloads in the past year

Rank #8,220 · ~9/day · ~266/mo

Releases R versions

Daily download trend is not available in this view yet.

30330 days

1.3K90 days

3.2K1 year

Compare downloads with other packages →

Also on432 r2u16 autocran

Repository

GitHub ↗ pllittle/cseqtl

3Stars

1Forks

0Open issues

0Open PRs

2Releases

30Commits

1Contributors

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

License GPL-3.0 · 30 commits · Last activity 2026-05-04

Stars over time

2024-02-18 · 32026-07-07 · 3

Repository practices

Upstream repositoryBeta

Checks run against github.com/pllittle/cseqtl on 2026-07-30.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

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.

Code & Tests

People & History

People (1)

Maintainer (1)

Paul Little

Author, Maintainer

Authors (1)

Paul Little

Author, Maintainer

Package Timeline

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

1.0.1Latest
2026-04-24 · current release · diff ↗
unarchivedReturned to CRAN
2026-04-24
R
R 4.6.0 released · 2026-04-24
archivedRemoved from CRAN
2026-04-13
issues were not corrected despite reminders
1.0.0
2026-03-10
R
R 4.5.0 released · 2025-04-11

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
Installed size: not tracked yet
With dependencies: not tracked yet

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