Package: scDotPlot 1.6.0

Benjamin I Laufer

scDotPlot: Cluster a Single-cell RNA-seq Dot Plot

Dot plots of single-cell RNA-seq data allow for an examination of the relationships between cell groupings (e.g. clusters) and marker gene expression. The scDotPlot package offers a unified approach to perform a hierarchical clustering analysis and add annotations to the columns and/or rows of a scRNA-seq dot plot. It works with SingleCellExperiment and Seurat objects as well as data frames.

Authors:Benjamin I Laufer [aut, cre], Brad A Friedman [aut]

scDotPlot_1.6.0.tar.gz
scDotPlot_1.6.0.zip(r-4.7-any)scDotPlot_1.6.0.zip(r-4.6-any)scDotPlot_1.6.0.zip(r-4.5-any)
scDotPlot_1.6.0.tgz(r-4.6-any)scDotPlot_1.6.0.tgz(r-4.5-any)
scDotPlot_1.6.0.tar.gz(r-4.7-any)scDotPlot_1.6.0.tar.gz(r-4.6-any)
scDotPlot_1.6.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
scDotPlot/json (API)

# Install 'scDotPlot' in R:

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

Bug tracker:https://github.com/ben-laufer/scdotplot/issues

On BioConductor:scDotPlot-1.7.0(bioc 3.24)scDotPlot-1.6.0(bioc 3.23)

software visualization differentialexpression geneexpression transcription rnaseq singlecell sequencing clustering

5.63 score 7 stars 61 scripts 320 downloads 1 exports 191 dependencies

Last updated from:8f805b873b (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.

Target	Result	Time	Files	Syslog
bioc-checks	NOTE	295
linux-devel	OK	716
source / vignettes	OK	449
linux-release	OK	488
macos-release	OK	342
macos-oldrel	OK	371
windows-devel	OK	1545
windows-release	OK	1415
windows-oldrel	OK	1330
wasm-release	OK	279

Exports:scDotPlot

Dependencies:abind ape aplot askpass assorthead base64enc beachmat beeswarm BH Biobase BiocGenerics BiocNeighbors BiocParallel BiocSingular bitops bslib cachem caTools cli cluster codetools commonmark cowplot cpp11 crosstalk curl data.table DelayedArray deldir digest dotCall64 dplyr dqrng evaluate farver fastDummies fastmap fitdistrplus FNN fontawesome fontBitstreamVera fontLiberation fontquiver formatR fs futile.logger futile.options future future.apply gdtools generics GenomicRanges ggbeeswarm ggfun ggiraph ggplot2 ggplotify ggrepel ggridges ggsci ggtree globals glue goftest gplots gridExtra gridGraphics gtable gtools here highr htmltools htmlwidgets httpuv httr ica igraph IRanges irlba isoband jquerylib jsonlite KernSmooth knitr labeling lambda.r later lattice lazyeval lifecycle listenv lmtest magrittr MASS Matrix MatrixGenerics matrixStats memoise mime miniUI nlme openssl otel parallelly patchwork pbapply pheatmap pillar pkgconfig plotly plyr png polyclip progressr promises purrr R6 RANN rappdirs RColorBrewer Rcpp RcppAnnoy RcppArmadillo RcppEigen RcppHNSW RcppML RcppProgress RcppTOML reshape2 reticulate rlang rmarkdown ROCR rprojroot RSpectra rsvd Rtsne S4Arrays S4Vectors S7 sass ScaledMatrix scales scater scattermore sctransform scuttle Seqinfo Seurat SeuratObject shiny SingleCellExperiment sitmo snow 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 tidytree tinytex treeio utf8 uwot vctrs vipor viridis viridisLite withr xfun xtable XVector yaml yulab.utils zoo

Introduction | Installation | SingleCellExperiment | Prepare object | Get features | Plot logcounts | Plot Z-scores | Seurat | Package support | Acknowledgement | Session info

Rendered fromscDotPlot.Rmdusingknitr::rmarkdown

Last update: 2024-09-17
Started: 2024-05-16

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
scDotPlot	scDotPlot scDotPlot.default scDotPlot.Seurat scDotPlot.SingleCellExperiment

Usage by other packages (reverse dependencies)