Package: chevreulShiny 1.5.0

Kevin Stachelek

chevreulShiny: Tools for managing SingleCellExperiment objects as projects

Tools for managing SingleCellExperiment objects as projects. Includes functions for analysis and visualization of single-cell data. Also included is a shiny app for visualization of pre-processed scRNA data. Supported by NIH grants R01CA137124 and R01EY026661 to David Cobrinik.

Authors:Kevin Stachelek [aut, cre], Bhavana Bhat [aut]

chevreulShiny_1.5.0.tar.gz
chevreulShiny_1.5.0.zip(r-4.7)chevreulShiny_1.5.0.zip(r-4.6)chevreulShiny_1.5.0.zip(r-4.5)
chevreulShiny_1.5.0.tgz(r-4.6-any)chevreulShiny_1.5.0.tgz(r-4.5-any)
chevreulShiny_1.5.0.tar.gz(r-4.7-any)chevreulShiny_1.5.0.tar.gz(r-4.6-any)
chevreulShiny_1.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
chevreulShiny/json (API)

# Install 'chevreulShiny' in R:

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

Bug tracker:https://github.com/cobriniklab/chevreulshiny/issues

Datasets:

cc.genes.cyclone - Cyclone cell cycle pairs by symbol
ensembl_version - Ensembl version used for build
grch38 - Human annotation data
grch38_tx2gene - Human transcripts to genes
human_to_mouse_homologs - Gene Homologs Between Human and Mouse
small_example_dataset - Small example SingleCellExperiment
tiny_sce - Tiny example SingleCellExperiment

On BioConductor:chevreulShiny-1.5.0(bioc 3.24)chevreulShiny-1.4.0(bioc 3.23)

coverage rnaseq sequencing visualization geneexpression transcription singlecell transcriptomics normalization preprocessing qualitycontrol dimensionreduction dataimport

4.30 score 5 scripts 5 exports 255 dependencies

Last updated from:fa7a9d5395. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	309
linux-devel-x86_64	NOTE	646
source / vignettes	OK	485
linux-release-x86_64	NOTE	644
macos-release-arm64	NOTE	387
macos-oldrel-arm64	NOTE	360
windows-devel	NOTE	517
windows-release	NOTE	475
windows-oldrel	NOTE	647
wasm-release	OK	311

Exports:list_plot_types load_bigwigs make_chevreul_clean_names minimalChevreulApp unite_metadata

Dependencies:abind alabaster.base alabaster.schemas AnnotationDbi AnnotationFilter askpass assertthat assorthead backports base64enc batchelor beachmat beeswarm BH Biobase BiocBaseUtils BiocGenerics BiocIO biocmake BiocNeighbors BiocParallel BiocSingular Biostrings bit bit64 bitops blob bluster brio bslib cachem callr checkmate chevreulPlot chevreulProcess cigarillo circlize cli clipr clue cluster clustree cmdfun codetools colorspace commonmark ComplexHeatmap cowplot cpp11 crayon credentials crosstalk curl data.table DataEditR DBI DelayedArray DelayedMatrixStats desc diffobj digest dir.expiry doParallel dplyr dqrng DT edgeR EnhancedVolcano EnsDb.Hsapiens.v86 ensembldb evaluate farver fastmap filelock FNN fontawesome forcats foreach formatR fs futile.logger futile.options future generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges gert GetoptLong ggbeeswarm ggforce ggplot2 ggplotify ggraph ggrepel gitcreds GlobalOptions globals glue graphlayouts gridExtra gridGraphics gtable highr hms htmltools htmlwidgets httpuv httr httr2 igraph ini IRanges irlba isoband iterators jquerylib jsonlite jsonvalidate KEGGREST knitr labeling lambda.r later lattice lazyeval lifecycle limma listenv litedown locfit magrittr markdown MASS Matrix MatrixGenerics matrixStats megadepth memoise metapod mime miniUI openssl otel parallelly patchwork pheatmap pillar pkgbuild pkgconfig pkgload plotly png polyclip praise prettyunits processx progress promises ProtGenerics ps purrr R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppML RcppProgress RCurl readr ResidualMatrix restfulr rhandsontable rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown rprojroot Rsamtools RSpectra RSQLite rstudioapi rsvd rtracklayer Rtsne S4Arrays S4Vectors S7 sass ScaledMatrix scales scater scran scuttle Seqinfo shape shiny shinyBS shinydashboard shinyFiles shinyhelper shinyjs shinyWidgets SingleCellExperiment sitmo snow sourcetools SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment sys systemfonts testthat tibble tidygraph tidyr tidyselect tinytex tweenr tzdb UCSC.utils usethis utf8 uwot V8 vctrs vipor viridis viridisLite vroom waiter waldo whisker wiggleplotr withr xfun XML xtable XVector yaml yulab.utils zip

chevreulShiny

Rendered fromchevreulShiny.Rmdusingknitr::rmarkdown

Last update: 2025-06-05
Started: 2024-10-23

Shiny App

Rendered fromshiny_app.Rmdusingknitr::rmarkdown

Last update: 2025-02-28
Started: 2024-10-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Update a database of chevreulShiny projects	append_to_project_db
Cyclone cell cycle pairs by symbol	cc.genes.cyclone
Create a shiny app for a project on disk	chevreulApp
Create a Table of single Cell Projects	create_proj_matrix
Create a database of chevreulShiny projects	create_project_db
Ensembl version used for build	ensembl_version
Get Transcripts in object	get_transcripts_from_sce
Human annotation data	grch38
Human transcripts to genes	grch38_tx2gene
Gene Homologs Between Human and Mouse	human_to_mouse_homologs
Collate list of variables to be plotted	list_plot_types
Load SingleCellExperiment Files from a single project path	load_alabaster_from_proj
Read in Gene and Transcript SingleCellExperiment Objects	load_alabaster_path
Load Bigwigs	load_bigwigs
Make Bigwig Database	make_bigwig_db
Clean Vector of chevreulShiny Names	make_chevreul_clean_names
Retrieve Metadata from Batch	metadata_from_batch
Create a minimal chevreulShiny app using SingleCellExperiment input	minimalChevreulApp
Plot BigWig Coverage for Genes of Interest by a Given Variable	plot_gene_coverage_by_var
Plotly settings	plotly_settings
Read a database of chevreulShiny projects	read_project_db
Save object to /output/sce/_sce.rds	save_sce
Small example SingleCellExperiment	small_example_dataset
Subset by new colData	subset_by_colData
Tiny example SingleCellExperiment	tiny_sce
Unite metadata	unite_metadata
Update a database of chevreulShiny projects	update_project_db