Package: scQTLtools 0.99.12

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/issues0 issues

Datasets:

On BioConductor:scQTLtools-0.99.11(bioc 3.21)

softwaregeneexpressiongeneticvariabilitysnpdifferentialexpressiongenomicvariationvariantdetectiongeneticsfunctionalgenomicssystemsbiologyregressionsinglecellnormalizationvisualizationrna-seqsc-eqtl

5.02 score 3 stars 123 downloads 40 exports 123 dependencies

Last updated 18 hours agofrom:58f5b0a695. Checks:1 OK, 6 ERROR. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 27 2025
R-4.5-winERRORMar 27 2025
R-4.5-macERRORMar 27 2025
R-4.5-linuxERRORMar 27 2025
R-4.4-winERRORMar 27 2025
R-4.4-macERRORMar 27 2025
R-4.4-linuxERRORMar 27 2025

Exports:adjust_pvaluesbuildZINBcallQTLcheckSNPListCPM_normalizecreateGeneLoccreateQTLObjectcreateSNPsLocDESeq_normalizedraw_boxplotdraw_histplotdraw_QTLplotdraw_violinplotfilter_by_abs_bfilterGeneSNPget_cell_groupsget_countsget_filter_dataget_model_infoget_raw_dataget_result_infoinitialize_progress_barlimma_normalizelinearModelload_biclassify_infoload_group_infoload_species_infolog_normalizenormalizeGeneplots_theme_optspoissonModelprocess_matrixremove_outliersset_filter_dataset_model_infoset_raw_dataset_result_infoTPM_normalizevisualizeQTLzinbModel

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocFileCacheBiocGenericsBiocParallelbiomaRtBiostringsbitbit64blobcachemclicodetoolscolorspacecpp11crayoncurlDBIdbplyrDelayedArrayDESeq2digestdotCall64dplyrfansifarverfastmapfilelockformatRfsfutile.loggerfutile.optionsfuturefuture.applygamlssgamlss.datagamlss.distgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2globalsglueGO.dbGOSemSimgtablehmshttrhttr2IRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelimmalistenvlocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslparallellypatchworkpillarpkgconfigplogrpngprettyunitsprogressprogressrpurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenrlangRSQLiteS4ArraysS4VectorsscalesSeuratObjectSingleCellExperimentsnowspspamSparseArraystatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectUCSC.utilsutf8vctrsVGAMviridisLitewithrxml2XVectoryulab.utils

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

Xiaofeng Wu, Xin Huang, Jingtong Kang, Siwen Xu

Rendered fromscQTLtools.Rmdusingknitr::rmarkdownon Mar 27 2025.

Last update: 2025-03-26
Started: 2024-08-13

Citation

scQTLtools can be cited as:

X Wu, X Huang, J Kang, S Xu

Corresponding BibTeX entry: 

  @Article{,
    title = {scQTLtools: An R package for single-cell eQTL analysis.},
    author = {Xiaofeng Wu and {Xin Huang} and {Jingtong Kang} and
      {Siwen Xu}},
    journal = {NULL},
    year = {2024},
    doi = {NULL},
  }

Readme and manuals

Help Manual

Help pageTopics
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 factordraw_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 factordraw_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 Valueget_cell_groups
Extract Counts from an Expression Matrixget_counts
Generic to access eQTLObject filter dataget_filter_data
Method to access eQTLObject filter dataget_filter_data,eQTLObject-method
Generic to access eQTLObject used model informationget_model_info
Method to access eQTLObject used model informationget_model_info,eQTLObject-method
Generic to access eQTLObject raw dataget_raw_data
Method to access eQTLObject raw dataget_raw_data,eQTLObject-method
Generic to access the result of identifying eQTLs from scRNA-seq dataget_result_info
Method to access the result of identifying eQTLs from scRNA-seq dataget_result_info,eQTLObject-method
Progress Bar for Model Analysis.initialize_progress_bar
Normalize the gene expression matrix with limmalimma_normalize
Linear model fitting the gene expression matrix and genotype matrix.linearModel
Generic to access eQTLObject biclassify informationload_biclassify_info
Method to access eQTLObject biclassify informationload_biclassify_info,eQTLObject-method
Generic to access eQTLObject cell grouping informationload_group_info
Method to access eQTLObject cell grouping informationload_group_info,eQTLObject-method
Generic to access eQTLObject species informationload_species_info
Method to access eQTLObject species informationload_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 plotsplots_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 frameprocess_matrix
Remove outliers from gene expression data and update cell listsremove_outliers
Generic to set eQTLObject filter dataset_filter_data
Method to set eQTLObject filter dataset_filter_data,eQTLObject-method
Generic to set eQTLObject used model informationset_model_info
Method to set eQTLObject used model informationset_model_info,eQTLObject-method
Generic to set eQTLObject raw dataset_raw_data
Method to set eQTLObject raw dataset_raw_data,eQTLObject-method
Generic to set the result of identifying eQTLs from scRNA-seq dataset_result_info
Method to set the result of identifying eQTLs from scRNA-seq dataset_result_info,eQTLObject-method
Show Method for eQTLObject Classshow,eQTLObject-method
Test eqtl objecttestEQTL
Test Gene Expression DatasettestGene
Test SeuratObjecttestSeurat
Test Genotype DatasettestSNP
Test Genotype DatasettestSNP2
Normalize the gene expression matrix with TPMTPM_normalize
visualizeQTL: Visualize the gene-snp pairs by group.visualizeQTL
Zinb model fitting the gene expression matrix.zinbModel