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scQTLtools

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

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


Bioconductor version: Development (3.22)

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

Maintainer: Xiaofeng Wu <1427972815 at qq.com>

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

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
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

Details

biocViews DifferentialExpression, FunctionalGenomics, GeneExpression, GeneticVariability, Genetics, GenomicVariation, Normalization, Preprocessing, Regression, SNP, SingleCell, Software, SystemsBiology, VariantDetection, Visualization
Version 1.1.5
In Bioconductor since BioC 3.21 (R-4.5) (< 6 months)
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), GOSemSim(>= 2.31.2)
System Requirements
URL https://github.com/XFWuCN/scQTLtools
Bug Reports https://github.com/XFWuCN/scQTLtools/issues
See More
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)
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Build Report Build Report

Package Archives

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

Source Package scQTLtools_1.1.5.tar.gz
Windows Binary (x86_64) scQTLtools_1.1.5.zip
macOS Binary (x86_64) scQTLtools_1.1.5.tgz
macOS Binary (arm64) scQTLtools_1.1.5.tgz
Source Repository git clone https://git.bioconductor.org/packages/scQTLtools
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scQTLtools
Bioc Package Browser https://code.bioconductor.org/browse/scQTLtools/
Package Short Url https://bioconductor.org/packages/scQTLtools/
Package Downloads Report Download Stats