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Bioconductor - scQTLtools

scQTLtools

This is the released version of scQTLtools; for the devel version, see scQTLtools.

An R package for single-cell eQTL analysis and visualization

Bioconductor version: Release (3.21)

This package specializes in analyzing and visualizing eQTL at the single-cell level. It can read gene expression matrices or Seurat data, or SingleCellExperiment object along with genotype data.

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")): Installation

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


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

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")
Details biocViews DifferentialExpression, FunctionalGenomics, GeneExpression, GeneticVariability, Genetics, GenomicVariation, Normalization, Regression, SNP, SingleCell, Software, SystemsBiology, VariantDetection, Visualization Version 1.0.3 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 Package Archives

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

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