Package: scRNAseqApp 1.12.0

Jianhong Ou

scRNAseqApp: A single-cell RNAseq Shiny app-package

The scRNAseqApp is a Shiny app package designed for interactive visualization of single-cell data. It is an enhanced version derived from the ShinyCell, repackaged to accommodate multiple datasets. The app enables users to visualize data containing various types of information simultaneously, facilitating comprehensive analysis. Additionally, it includes a user management system to regulate database accessibility for different users.

Authors:Jianhong Ou [aut, cre]

scRNAseqApp_1.12.0.tar.gz
scRNAseqApp_1.12.0.zip(r-4.7)scRNAseqApp_1.12.0.zip(r-4.6)scRNAseqApp_1.12.0.zip(r-4.5)
scRNAseqApp_1.12.0.tgz(r-4.6-any)scRNAseqApp_1.12.0.tgz(r-4.5-any)
scRNAseqApp_1.12.0.tar.gz(r-4.7-any)scRNAseqApp_1.12.0.tar.gz(r-4.6-any)
scRNAseqApp_1.12.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
scRNAseqApp/json (API)
NEWS

# Install 'scRNAseqApp' in R:

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

Bug tracker:https://github.com/jianhong/scrnaseqapp/issues

On BioConductor:scRNAseqApp-1.13.2(bioc 3.24)scRNAseqApp-1.12.0(bioc 3.23)

visualization singlecell rnaseq interactive-visualizations multiple-users shiny-apps single-cell-rna-seq

5.84 score 6 stars 4 scripts 338 downloads 11 exports 228 dependencies

Last updated from:96c8478c98 (on RELEASE_3_23). Checks:1 WARNING, 3 ERROR, 6 OK. Indexed: no.

Target	Result	Time
bioc-checks	WARNING	328
linux-devel-x86_64	ERROR	622
source / vignettes	OK	382
linux-release-x86_64	ERROR	584
macos-release-arm64	OK	365
macos-oldrel-arm64	OK	306
windows-devel	ERROR	672
windows-release	OK	580
windows-oldrel	OK	672
wasm-release	OK	270

Exports:APPconf as.list availableThemes createAppConfig createDataSet extractFragmentNameMapList lapply markers scInit scRNAseqApp show

Dependencies:abind askpass assertthat backports base64enc BH bibtex billboarder Biobase BiocGenerics BiocIO biocmake BiocParallel Biostrings bit bit64 bitops blob bslib cachem caTools checkmate cigarillo circlize cli clue cluster codetools colorspace colourpicker commonmark ComplexHeatmap cowplot cpp11 crayon crosstalk curl data.table DBI DelayedArray deldir desc digest dir.expiry doParallel dotCall64 dplyr dqrng DT evaluate farver fastDummies fastmap filelock fitdistrplus FNN fontawesome foreach formatR fs futile.logger futile.options future future.apply generics GenomeInfoDb GenomicAlignments GenomicRanges GetoptLong ggdendro ggforce ggnewscale ggplot2 ggrepel ggridges GlobalOptions globals glue goftest gplots gridExtra gtable gtools here highr htmltools htmlwidgets httpuv httr ica igraph IRanges irlba isoband iterators jquerylib jsonlite KernSmooth knitr labeling lambda.r later lattice lazyeval learnr lifecycle listenv litedown lmtest lubridate magrittr markdown MASS Matrix MatrixGenerics matrixStats memoise mime miniUI nlme openssl otel parallelly patchwork pbapply pillar pkgconfig plotly plyr png polyclip princurve progressr promises purrr R.methodsS3 R.oo R.utils R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppProgress RcppTOML RCurl RefManageR renv reshape2 restfulr reticulate rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown ROCR rprojroot Rsamtools RSpectra RSQLite rtracklayer Rtsne S4Arrays S4Vectors S7 sass scales scattermore scrypt sctransform Seqinfo Seurat SeuratObject shape shiny shinyhelper shinyjs shinymanager SingleCellExperiment sitmo slingshot snow sortable sourcetools sp spam SparseArray spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringi stringr SummarizedExperiment survival sys systemfonts tensor tibble tidyr tidyselect timechange tinytex TrajectoryUtils tweenr UCSC.utils utf8 uwot vctrs viridisLite withr xfun XML xml2 xtable XVector yaml zoo

scRNAseqApp Guide

Jianhong Ou

Rendered fromscRNAseqApp.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-02-12
Started: 2022-12-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Class '"APPconf"'	APPconf APPconf-class
The methods for APPconf-class	$,APPconf-method $<-,APPconf-method APPconf-methods as.character,APPconf-method as.list,APPconf-method lapply,APPconf-method markers markers,APPconf-method show,APPconf-method unlist,APPconf-method [,APPconf,ANY,ANY,ANY-method [[,APPconf,ANY,ANY-method [[<-,APPconf,ANY,ANY,ANY-method
Available themes of color sets	availableThemes
Create a metadata to describe the dataset	createAppConfig
Create a dataset Create a dataset from a Seurat object. The function will try to find the markers in the Misc data named as 'markers'. The misc data should be output of function 'FindAllMarkers'.	createDataSet
load data from cellRanger	createSeuFromCellRanger
load data from a count matrix	createSeuFromMatrix
Extract fragment name map	extractFragmentNameMapList
Create a scRNAseqApp project	scInit
scRNAseqApp main function	scRNAseqApp