Package: SeuratExplorer 0.1.9

SeuratExplorer: An 'Shiny' App for Exploring scRNA-seq Data Processed in 'Seurat'

A simple, one-command package which runs an interactive dashboard capable of common visualizations for single cell RNA-seq. 'SeuratExplorer' requires a processed 'Seurat' object, which is saved as 'rds' or 'qs2' file.

Authors:Yongchao Zhang [aut, cre]

SeuratExplorer_0.1.9.tar.gz
SeuratExplorer_0.1.9.zip(r-4.7-any)SeuratExplorer_0.1.9.zip(r-4.6-any)SeuratExplorer_0.1.9.zip(r-4.5-any)
SeuratExplorer_0.1.9.tgz(r-4.6-any)SeuratExplorer_0.1.9.tgz(r-4.5-any)
SeuratExplorer_0.1.9.tar.gz(r-4.7-any)SeuratExplorer_0.1.9.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
SeuratExplorer/json (API)

# Install 'SeuratExplorer' in R:

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

Bug tracker:https://github.com/fentouxungui/seuratexplorer/issues

Datasets:

GenesDB - Genes information extracted from genome gtf file

On CRAN:

5.16 score 9 stars 12 scripts 423 downloads 10 exports 161 dependencies

Last updated from:f353c4f9d5. Checks:7 WARNING, 1 OK, 1 FAIL. Indexed: yes.

Target	Result	Time
linux-devel	WARNING	250
source / vignettes	OK	211
linux-release	WARNING	275
macos-release	WARNING	233
macos-oldrel	WARNING	189
windows-devel	WARNING	217
windows-release	WARNING	242
windows-oldrel	WARNING	153
wasm-release	FAIL	146

Exports:cellRatioPlot explorer_body_ui explorer_server explorer_sidebar_ui getColors launchSeuratExplorer param_group_collapse server top_genes ui

Dependencies:abind askpass base64enc BH bitops bslib cachem caTools circlize cli cluster codetools colorspace colourpicker commonmark cowplot cpp11 crosstalk curl data.table deldir digest dotCall64 dplyr dqrng DT evaluate farver fastDummies fastmap fitdistrplus FNN fontawesome fs future future.apply generics ggalluvial ggplot2 ggrepel ggridges GlobalOptions globals glue goftest gplots gridExtra gtable gtools here highr htmltools htmlwidgets httpuv httr ica igraph irlba isoband jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval lifecycle listenv litedown lmtest magrittr markdown MASS Matrix matrixStats memoise mime miniUI nlme openssl otel parallelly patchwork pbapply pillar pkgconfig plotly plyr png polyclip progressr promises purrr qs2 R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppParallel RcppProgress RcppThread RcppTOML reshape2 reticulate rlang rmarkdown ROCR rprojroot RSpectra Rtsne S7 sass scales scattermore sctransform Seurat SeuratObject shape shiny shinyBS shinycssloaders shinydashboard shinyjqui shinyjs shinyWidgets sitmo sourcetools sp spam spatstat.data spatstat.explore spatstat.geom spatstat.random spatstat.sparse spatstat.univar spatstat.utils stringfish stringi stringr survival sys tensor tibble tidyr tidyselect tinytex utf8 uwot vctrs viridisLite withr xfun xtable yaml zoo

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
plot cell percentage barplot	cellRatioPlot
generate the body UI for each menu item specified in 'explorer_sidebar_ui'	explorer_body_ui
server side functions related to 'explorer_sidebar_ui'	explorer_server
some menu items of the dashboard sidebar	explorer_sidebar_ui
Genes information extracted from genome gtf file	GenesDB
Helper function to extract counts matrix with proper handling	get_counts_matrix
Helper function to extract data matrix with proper handling	get_data_matrix
getColors	getColors
Helper function to join layers for Assay5 objects	join_layers_if_needed
Launch shiny app	launchSeuratExplorer
Create a collapsible parameter group for Plot Settings	param_group_collapse
extract the features from row names or annotation slot of assays	prepare_gene_annotations
Server	server
Find Top Genes by Cell	top_genes
UI	ui