Package: DOtools 1.2.0

Mariano Ruz Jurado

DOtools: Convenient functions to streamline your single cell data analysis workflow

This package provides functions for creating various visualizations, convenient wrappers, and quality-of-life utilities for single cell experiment objects. It offers a streamlined approach to visualize results and integrates different tools for easy use.

Authors:Mariano Ruz Jurado [aut, cre], David Rodriguez Morales [aut], David John [aut], DFG SFB 1366, Project B04 [fnd], DFG SFB 1531, Project 456687919 [fnd]

DOtools_1.2.0.tar.gz
DOtools_1.2.0.zip(r-4.7)DOtools_1.2.0.zip(r-4.6)DOtools_1.2.0.zip(r-4.5)
DOtools_1.2.0.tgz(r-4.6-any)DOtools_1.2.0.tgz(r-4.5-any)
DOtools_1.2.0.tar.gz(r-4.7-any)DOtools_1.2.0.tar.gz(r-4.6-any)
DOtools_1.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
DOtools/json (API)
NEWS

# Install 'DOtools' in R:

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

Bug tracker:https://github.com/marianoruzjurado/dotools/issues

Pkgdown/docs site:https://marianoruzjurado.github.io

On BioConductor:DOtools-1.3.0(bioc 3.24)DOtools-1.2.0(bioc 3.23)

singlecell rnaseq visualization clustering annotation workflowstep qualitycontrol geneexpression

6.14 score 6 stars 22 scripts 186 downloads 24 exports 330 dependencies

Last updated from:45b027e774 (on RELEASE_3_23). Checks:1 WARNING, 4 NOTE, 2 OK, 3 ERROR. Indexed: no.

Target	Result	Time
bioc-checks	WARNING	300
linux-devel-x86_64	NOTE	2417
source / vignettes	OK	2329
linux-release-x86_64	NOTE	2417
macos-release-arm64	NOTE	1287
macos-oldrel-arm64	NOTE	1573
windows-devel	ERROR	1269
windows-release	ERROR	1258
windows-oldrel	ERROR	1220
wasm-release	OK	264

Exports:DO.Barplot DO.BarplotClustert DO.BoxPlot DO.CellBender DO.CellComposition DO.CellTypist DO.Correlation DO.DietSCE DO.Dotplot DO.enrichR DO.EvalIntegration DO.FullRecluster DO.Heatmap DO.HeatmapFC DO.Import DO.Integration DO.MultiDGE DO.PyEnv DO.scVI DO.SplitBarGSEA DO.Subset DO.TransferLabel DO.UMAP DO.VlnPlot

Dependencies:abind askpass assorthead backports base64enc basilisk beachmat beeswarm BH Biobase BiocGenerics BiocIO biocmake BiocNeighbors BiocParallel BiocSingular Biostrings bit bit64 bitops blob bluster boot broom bslib cachem Cairo callr car carData caTools cellranger cigarillo circlize cli clipr cluster codetools colorspace commonmark conflicted corrplot cowplot cpp11 crayon crosstalk curl data.table datawizard DBI dbplyr DelayedArray DelayedMatrixStats deldir Deriv DESeq2 digest dir.expiry doBy dotCall64 dplyr dqrng DropletUtils dtplyr edgeR enrichR evaluate farver fastDummies fastmap filelock fitdistrplus FNN fontawesome fontBitstreamVera fontLiberation fontquiver forcats forecast formatR Formula fracdiff fs futile.logger futile.options future future.apply gargle gdtools generics GenomeInfoDb GenomicAlignments GenomicRanges ggalluvial ggbeeswarm ggcorrplot ggiraph ggiraphExtra ggplot2 ggprism ggpubr ggrastr ggrepel ggridges ggsci ggsignif ggtext GlobalOptions globals glue goftest googledrive googlesheets4 gplots gridExtra gridtext gtable gtools h5mread haven HDF5Array here highr hms htmltools htmlwidgets httpuv httr ica ids igraph insight IRanges irlba isoband janitor jpeg jquerylib jsonlite kernlab KernSmooth knitr ks labeling lambda.r later lattice lazyeval lifecycle limma listenv litedown lme4 lmtest locfit lubridate magrittr markdown MASS Matrix MatrixGenerics MatrixModels matrixStats mclust mcprogress memoise metapod mgcv microbenchmark mime miniUI minqa modelr multicool mvtnorm mycor nlme nloptr nnet numDeriv openssl openxlsx otel paletteer parallelly patchwork pbapply pbkrtest pheatmap pillar pkgconfig plotly plyr png polyclip polynom ppcor pracma prettyunits prismatic processx progress progressr promises ps purrr quantreg R.methodsS3 R.oo R.utils R6 ragg RANN rappdirs rbibutils RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppML RcppProgress RcppTOML RCurl Rdpack readr readxl reformulas rematch rematch2 reprex reshape2 restfulr reticulate rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown ROCR rprojroot Rsamtools RSpectra rstatix rstudioapi rsvd rtracklayer Rtsne rvest S4Arrays S4Vectors S7 sass ScaledMatrix scales scater scattermore scCustomize scDblFinder SCpubr scran sctransform scuttle selectr Seqinfo Seurat SeuratObject shape shiny SingleCellExperiment sitmo sjlabelled sjmisc snakecase snow sourcetools sp spam SparseArray SparseM sparseMatrixStats spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils statmod stringi stringr SummarizedExperiment survival sys systemfonts tensor textshaping tibble tidyr tidyselect tidyverse timechange timeDate tinytex tzdb UCSC.utils urca utf8 uuid uwot vctrs vipor viridis viridisLite vroom withr WriteXLS xfun xgboost XML xml2 xtable XVector yaml zellkonverter zip zoo

Quality control of sc/snRNA-seq

Mariano Ruz Jurado

Rendered fromDOtools.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2026-04-13
Started: 2025-06-18

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
SEM Graph with wilcox test on single cell level	DO.Barplot
SEM Graph with t test on cluster level	DO.BarplotClustert
Box Graph with wilcox test on single cell level	DO.BoxPlot
DO.CellBender	DO.CellBender
DO CellComposition	DO.CellComposition
DO Celltypist	DO.CellTypist
DO Correlation Plot for visualizing similarity between categories	DO.Correlation
Remove Layers from Seurat or SCE Object by Pattern	DO.DietSCE
DO Dot plot	DO.Dotplot
DO.enrichR	DO.enrichR
Do batch correction metrics for integration	DO.EvalIntegration
DO.FullRecluster	DO.FullRecluster
DO Heatmap of the mean expression of genes across a groups	DO.Heatmap
DO Heatmap of the mean expression of genes across a groups	DO.HeatmapFC
DO.Import	DO.Import
DO.Integration SCE object integration directly	DO.Integration
DO.MultiDGE	DO.MultiDGE
DO.PyEnv	DO.PyEnv
DO.scVI	DO.scVI
DO Bar plot for GSEA df result	DO.SplitBarGSEA
DO.Subset	DO.Subset
DO.TransferLabel	DO.TransferLabel
DO.UMAP	DO.UMAP
Violin Graph with wilcox test on single cell level	DO.VlnPlot
DOtools: A Toolkit for scRNA Data Analysis	DOtools