scQTLtools

This is the development version of scQTLtools; for the stable release version, see scQTLtools.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21

scQTLtools: an R/Bioconductor package for comprehensive identification and visualization of single-cell eQTLs

Bioconductor version: Development (3.24)

scQTLtools is a comprehensive R/Bioconductor package that facilitates end-to-end single-cell eQTL analysis, from preprocessing to visualization

Author: Xiaofeng Wu [aut, cre, cph] ORCID: 0009-0003-6254-5575 , Xin Huang [aut, cph] ORCID: 0009-0005-2755-0357 , Jingtong Kang [com] ORCID: 0009-0008-8343-3456 , Siwen Xu [aut, cph] ORCID: 0000-0001-7936-0639

Maintainer: Xiaofeng Wu <1427972815 at qq.com>

Citation (from within R, enter citation("scQTLtools")):

Xiaofeng Wu, Xin Huang, Siwen Xu. scQTLtools: scQTLtools: an R/Bioconductor package for comprehensive identification and visualization of single-cell eQTLs. doi:10.18129/B9.bioc.scQTLtools, R package version 1.5.0, https://bioconductor.org/packages/scQTLtools.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("scQTLtools")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("scQTLtools")

scQTLtools: an R/Bioconductor package for comprehensive identification and visualization of single-cell eQTLs	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, FunctionalGenomics, GeneExpression, GeneticVariability, Genetics, GenomicVariation, Normalization, Preprocessing, Regression, SNP, SingleCell, Software, SystemsBiology, VariantDetection, Visualization
Version	1.5.0
In Bioconductor since	BioC 3.21 (R-4.5) (1.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.4.1.0)
Imports	ggplot2 (>= 3.5.1), Matrix (>= 1.7-0), stats (>= 4.4.1), progress (>= 1.2.3), stringr (>= 1.5.1), dplyr (>= 1.1.4), SeuratObject (>= 5.0.2), methods (>= 4.4.1), magrittr (>= 2.0.3), patchwork (>= 1.2.0), DESeq2 (>= 1.45.3), VGAM (>= 1.1-11), limma (>= 3.61.9), biomaRt (>= 2.61.3), gamlss (>= 5.4-22), SingleCellExperiment (>= 1.27.2), SummarizedExperiment (>= 1.32.0), yulab.utils (>= 0.2.3)
System Requirements
URL	https://github.com/XFWuCN/scQTLtools
Bug Reports	https://github.com/XFWuCN/scQTLtools/issues

Suggests	BiocStyle, knitr, rmarkdown, org.Hs.eg.db, org.Mm.eg.db, org.Ce.eg.db, org.At.tair.db, testthat (>= 3.2.1.1)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
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Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	scQTLtools_1.5.0.tar.gz
Windows Binary (x86_64)	scQTLtools_1.5.0.zip
macOS Binary (big-sur-x86_64)	scQTLtools_1.5.0.tgz
macOS Binary (sonoma-arm64)	scQTLtools_1.5.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scQTLtools
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scQTLtools
Package Short Url	https://bioconductor.org/packages/scQTLtools/
Package Downloads Report	Download Stats