Package: scQTLtools 0.99.11

Xiaofeng Wu

scQTLtools: An R package for single-cell eQTL analysis and visualization

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.

Authors:Xiaofeng Wu [aut, cre, cph], Xin Huang [aut, cph], Jingtong Kang [com], Siwen Xu [aut, cph]

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scQTLtools.pdf |scQTLtools.html✨
scQTLtools/json (API)
NEWS

# Install 'scQTLtools' in R:

install.packages('scQTLtools', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/xfwucn/scqtltools/issues

Datasets:

testEQTL - Test eqtl object
testGene - Test Gene Expression Dataset
testSNP - Test Genotype Dataset
testSNP2 - Test Genotype Dataset
testSeurat - Test SeuratObject

On BioConductor:scQTLtools-0.99.11(bioc 3.21)

software geneexpression geneticvariability snp differentialexpression genomicvariation variantdetection genetics functionalgenomics systemsbiology regression singlecell normalization visualization rna-seq sc-eqtl

4.48 score 1 stars 40 exports 123 dependencies

Last updated 1 months agofrom:ea832403d6. Checks:5 OK, 1 WARNING. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 31 2025
R-4.5-win	OK	Jan 31 2025
R-4.5-mac	WARNING	Jan 31 2025
R-4.5-linux	OK	Jan 31 2025
R-4.4-win	OK	Jan 31 2025
R-4.4-mac	OK	Jan 31 2025

Exports:adjust_pvalues buildZINB callQTL checkSNPList CPM_normalize createGeneLoc createQTLObject createSNPsLoc DESeq_normalize draw_boxplot draw_histplot draw_QTLplot draw_violinplot filter_by_abs_b filterGeneSNP get_cell_groups get_counts get_filter_data get_model_info get_raw_data get_result_info initialize_progress_bar limma_normalize linearModel load_biclassify_info load_group_info load_species_info log_normalize normalizeGene plots_theme_opts poissonModel process_matrix remove_outliers set_filter_data set_model_info set_raw_data set_result_info TPM_normalize visualizeQTL zinbModel

Dependencies:abind AnnotationDbi askpass BH Biobase BiocFileCache BiocGenerics BiocParallel biomaRt Biostrings bit bit64 blob cachem cli codetools colorspace cpp11 crayon curl DBI dbplyr DelayedArray DESeq2 digest dotCall64 dplyr fansi farver fastmap filelock formatR fs futile.logger futile.options future future.apply gamlss gamlss.data gamlss.dist generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 globals glue GO.db GOSemSim gtable hms httr httr2 IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle limma listenv locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl parallelly patchwork pillar pkgconfig plogr png prettyunits progress progressr purrr R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen rlang RSQLite S4Arrays S4Vectors scales SeuratObject SingleCellExperiment snow sp spam SparseArray statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect UCSC.utils utf8 vctrs VGAM viridisLite withr xml2 XVector yulab.utils

scQTLtools:An R package for single-cell eQTL analysis.

Xiaofeng Wu, Xin Huang, Jingtong Kang, Siwen Xu

Rendered fromscQTLtools.Rmdusingknitr::rmarkdownon Jan 31 2025.

Last update: 2025-01-15
Started: 2024-08-13

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Adjust p-values and perform threshold filtering based on the adjusted p-values.	adjust_pvalues
Build zinb model.	buildZINB
callQTL: Uncover single-cell eQTLs exclusively using scRNA-seq data. A function designed to identify eQTLs from scRNA-seq data.	callQTL
Check if the SNP ids in the input genotype matrix are valid.	checkSNPList
Normalize the gene expression matrix with CPM.	CPM_normalize
Create gene location dataframe.	createGeneLoc
createObject:Create the eQTLObject. We next create a S4 object. The object serves as a container that contains both data (like the count matrix) and meta.data.	createQTLObject
Create SNP location dataframe.	createSNPsLoc
Normalize the gene expression matrix with DESeq.	DESeq_normalize
Generate a boxplot of expression levels by SNP factor	draw_boxplot
Generate a hist plot of expression levels by SNP factor.	draw_histplot
Create a combined plot with violin, boxplot, and scatter point overlay.	draw_QTLplot
Generate a violin plot of expression levels by SNP factor	draw_violinplot
Class 'eQTLObject' The eQTLObject class is an R object designed to store data related to eQTL analysis, encompassing data lists, result data frames, and layers for biClassify, species, and grouping information.	eQTLObject-class
Filters data frame by absolute b-values, returning rows meeting or exceeding a threshold.	filter_by_abs_b
filterGeneSNP: Filter gene expression matrix and genotype matrix.	filterGeneSNP
Retrieve Cells by SNP Value	get_cell_groups
Extract Counts from an Expression Matrix	get_counts
Generic to access eQTLObject filter data	get_filter_data
Method to access eQTLObject filter data	get_filter_data,eQTLObject-method
Generic to access eQTLObject used model information	get_model_info
Method to access eQTLObject used model information	get_model_info,eQTLObject-method
Generic to access eQTLObject raw data	get_raw_data
Method to access eQTLObject raw data	get_raw_data,eQTLObject-method
Generic to access the result of identifying eQTLs from scRNA-seq data	get_result_info
Method to access the result of identifying eQTLs from scRNA-seq data	get_result_info,eQTLObject-method
Progress Bar for Model Analysis.	initialize_progress_bar
Normalize the gene expression matrix with limma	limma_normalize
Linear model fitting the gene expression matrix and genotype matrix.	linearModel
Generic to access eQTLObject biclassify information	load_biclassify_info
Method to access eQTLObject biclassify information	load_biclassify_info,eQTLObject-method
Generic to access eQTLObject cell grouping information	load_group_info
Method to access eQTLObject cell grouping information	load_group_info,eQTLObject-method
Generic to access eQTLObject species information	load_species_info
Method to access eQTLObject species information	load_species_info,eQTLObject-method
Normalize the gene expression matrix with logNormalize method.	log_normalize
normalizeGene: Normalize the gene expression data.	normalizeGene
Theme options for customized plots	plots_theme_opts
Poisson model fitting the gene expression matrix and genotype matrix.	poissonModel
Process a matrix to extract a row and convert it to a data frame	process_matrix
Remove outliers from gene expression data and update cell lists	remove_outliers
Generic to set eQTLObject filter data	set_filter_data
Method to set eQTLObject filter data	set_filter_data,eQTLObject-method
Generic to set eQTLObject used model information	set_model_info
Method to set eQTLObject used model information	set_model_info,eQTLObject-method
Generic to set eQTLObject raw data	set_raw_data
Method to set eQTLObject raw data	set_raw_data,eQTLObject-method
Generic to set the result of identifying eQTLs from scRNA-seq data	set_result_info
Method to set the result of identifying eQTLs from scRNA-seq data	set_result_info,eQTLObject-method
Show Method for eQTLObject Class	show,eQTLObject-method
Test eqtl object	testEQTL
Test Gene Expression Dataset	testGene
Test SeuratObject	testSeurat
Test Genotype Dataset	testSNP
Test Genotype Dataset	testSNP2
Normalize the gene expression matrix with TPM	TPM_normalize
visualizeQTL: Visualize the gene-snp pairs by group.	visualizeQTL
Zinb model fitting the gene expression matrix.	zinbModel