Package: tenXplore 1.35.0

VJ Carey

tenXplore: ontological exploration of scRNA-seq of 1.3 million mouse neurons from 10x genomics

Perform ontological exploration of scRNA-seq of 1.3 million mouse neurons from 10x genomics.

Authors:Vince Carey

tenXplore_1.35.0.tar.gz
tenXplore_1.35.0.zip(r-4.7)tenXplore_1.35.0.zip(r-4.6)tenXplore_1.35.0.zip(r-4.5)
tenXplore_1.35.0.tgz(r-4.6-any)tenXplore_1.35.0.tgz(r-4.5-any)
tenXplore_1.35.0.tar.gz(r-4.7-any)tenXplore_1.35.0.tar.gz(r-4.6-any)
tenXplore_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
tenXplore/json (API)

# Install 'tenXplore' in R:

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

Datasets:

CellTypes - CellTypes: data.frame with ids and terms
tenx500 - Tenx500: serialized full SummarizedExperiment for demonstration

On BioConductor:tenXplore-1.35.0(bioc 3.24)tenXplore-1.34.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncology dimensionreduction principalcomponent transcriptomics singlecell

4.00 score 8 scripts 416 downloads 2 exports 115 dependencies

Last updated from:dea7f9cf57. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time	Files	Syslog
bioc-checks	ERROR	278
linux-devel-x86_64	NOTE	421
source / vignettes	OK	272
linux-release-x86_64	NOTE	374
macos-release-arm64	NOTE	378
macos-oldrel-arm64	NOTE	248
windows-devel	NOTE	318
windows-release	NOTE	340
windows-oldrel	NOTE	367
wasm-release	OK	206

Exports:se1.3M tenXplore

Dependencies:abind AnnotationDbi AnnotationHub askpass base64enc basilisk BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocManager BiocVersion Biostrings bit bit64 blob bslib cachem cli commonmark coro cpp11 crayon crosstalk curl DBI dbplyr DelayedArray digest dir.expiry dplyr DT ellmer evaluate fastmap filelock fontawesome fs generics GenomicRanges glue graph here highr htmltools htmlwidgets httpuv httr httr2 igraph IRanges jquerylib jsonlite KEGGREST knitr later lattice lazyeval lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime ontologyIndex ontologyPlot ontoProc openssl org.Mm.eg.db otel paintmap pillar pkgconfig png promises purrr R.methodsS3 R.oo R.utils R6 rappdirs RBGL Rcpp RcppTOML reticulate Rgraphviz rlang rmarkdown rprojroot RSQLite S4Arrays S4Vectors S7 sass Seqinfo shiny sourcetools SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex utf8 vctrs withr xfun xtable XVector yaml

tenXplore: ontology for scRNA-seq, applied to 10x 1.3 million neurons

Introduction/Executive summary | A challenge: finding expression signatures of anatomic structures or cell types | Discrimination of neuron types: exploratory multivariate analysis | Next steps

Rendered fromtenXplore.Rmdusingknitr::rmarkdown

Last update: 2019-06-13
Started: 2017-08-22

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
cellTypes: data.frame with ids and terms	CellTypes
add/retrieve HSDS-based SE to/from cache	se1.3M
tenx500: serialized full SummarizedExperiment for demonstration	tenx500
basic shiny interface to 10x data with ontological setup for cell selection	tenXplore

Usage by other packages (reverse dependencies)