scQTLtools
This is the development version of scQTLtools; for the stable release version, see scQTLtools.
An R package for single-cell eQTL analysis and visualization
Bioconductor version: Development (3.22)
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. It offers a function for cis-eQTL analysis to detect eQTL within a given range, and another function to fit models with three methods. Using this package, users can also generate single-cell level visualization result.
Author: Xiaofeng Wu [aut, cre, cph]
, Xin Huang [aut, cph]
, Jingtong Kang [com]
, Siwen Xu [aut, cph]
Maintainer: Xiaofeng Wu <1427972815 at qq.com>
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 package for single-cell eQTL analysis. | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, FunctionalGenomics, GeneExpression, GeneticVariability, Genetics, GenomicVariation, Normalization, Regression, SNP, SingleCell, Software, SystemsBiology, VariantDetection, Visualization |
| Version | 1.1.1 |
| 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) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scQTLtools_1.1.1.tar.gz |
| Windows Binary (x86_64) | scQTLtools_1.1.1.zip |
| macOS Binary (x86_64) | scQTLtools_1.1.1.tgz |
| macOS Binary (arm64) | scQTLtools_1.1.1.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 |