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 (3.24)
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]
, Xin Huang [aut, cph]
, Jingtong Kang [com]
, Siwen Xu [aut, cph]
Maintainer: Xiaofeng Wu <1427972815 at qq.com>
citation("scQTLtools")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 | ||
| NEWS | Text | |
| LICENSE | Text |
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 |
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_1.5.0.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/scQTLtools/ |
| Package Short Url | https://bioconductor.org/packages/scQTLtools/ |
| Package Downloads Report | Download Stats |