Package: scRNAseqApp 1.7.6

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_1.7.6.tar.gz

scRNAseqApp_1.7.6.tgz(r-4.4-any)scRNAseqApp_1.7.6.tgz(r-4.3-any)
scRNAseqApp_1.7.6.tar.gz(r-4.5-noble)scRNAseqApp_1.7.6.tar.gz(r-4.4-noble)
scRNAseqApp_1.7.6.tgz(r-4.4-emscripten)
scRNAseqApp.pdf |scRNAseqApp.html✨
scRNAseqApp/json (API)
NEWS

# Install 'scRNAseqApp' in R:

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

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

On BioConductor:scRNAseqApp-1.7.6(bioc 3.21)scRNAseqApp-1.6.0(bioc 3.20)

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

5.78 score 4 stars 3 scripts 164 downloads 9 exports 226 dependencies

Last updated 1 months agofrom:ca33026a20. Checks:OK: 2 NOTE: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 22 2024
R-4.5-linux	OK	Dec 22 2024
R-4.4-mac	NOTE	Dec 22 2024
R-4.3-mac	NOTE	Dec 22 2024

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

Dependencies:abind askpass assertthat backports base64enc BH bibtex billboarder Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob bslib cachem caTools checkmate circlize cli clue cluster codetools colorspace colourpicker commonmark ComplexHeatmap cowplot cpp11 crayon crosstalk curl data.table DBI DelayedArray deldir digest doParallel dotCall64 dplyr dqrng DT ellipsis evaluate fansi farver fastDummies fastmap fitdistrplus FNN fontawesome foreach formatR fs futile.logger futile.options future future.apply generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges GetoptLong ggdendro ggforce 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 leiden lifecycle listenv lmtest lubridate magrittr markdown MASS Matrix MatrixGenerics matrixStats memoise mgcv mime miniUI munsell nlme openssl parallelly patchwork pbapply pillar pkgconfig plogr 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 sass scales scattermore scrypt sctransform 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 zlibbioc zoo

scRNAseqApp Guide

Jianhong Ou

Rendered fromscRNAseqApp.Rmdusingknitr::rmarkdownon Dec 22 2024.

Last update: 2024-03-15
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
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
Create a scRNAseqApp project	scInit
scRNAseqApp main function	scRNAseqApp