Package: tomoseqr 1.17.0

Ryosuke Matsuzawa

tomoseqr: R Package for Analyzing Tomo-seq Data

`tomoseqr` is an R package for analyzing Tomo-seq data. Tomo-seq is a genome-wide RNA tomography method that combines combining high-throughput RNA sequencing with cryosectioning for spatially resolved transcriptomics. `tomoseqr` reconstructs 3D expression patterns from tomo-seq data and visualizes the reconstructed 3D expression patterns.

Authors:Ryosuke Matsuzawa [aut, cre]

tomoseqr_1.17.0.tar.gz
tomoseqr_1.17.0.zip(r-4.7)tomoseqr_1.17.0.zip(r-4.6)tomoseqr_1.17.0.zip(r-4.5)
tomoseqr_1.17.0.tgz(r-4.6-any)tomoseqr_1.17.0.tgz(r-4.5-any)
tomoseqr_1.17.0.tar.gz(r-4.7-any)tomoseqr_1.17.0.tar.gz(r-4.6-any)
tomoseqr_1.17.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
tomoseqr/json (API)
NEWS

# Install 'tomoseqr' in R:
install.packages('tomoseqr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • mask - A matrix containing mask data.
  • testx - A data.frame object containing a simulated Tomo-seq data for x-axis sections.
  • testy - A data.frame object containing a simulated Tomo-seq data for y-axis sections.
  • testz - A data.frame object containing a simulated Tomo-seq data for z-axis sections.
  • tomoObj - A tomoSeq object.

On BioConductor:tomoseqr-1.17.0(bioc 3.24)tomoseqr-1.16.0(bioc 3.23)

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

geneexpressionsequencingrnaseqtranscriptomicsspatialvisualizationsoftware

4.32 score 21 scripts 322 downloads 13 exports 88 dependencies

Last updated from:1260025816. Checks:1 WARNING, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING204
linux-devel-x86_64OK270
source / vignettesOK227
linux-release-x86_64OK292
macos-release-arm64OK128
macos-oldrel-arm64OK142
windows-develOK216
windows-releaseOK141
windows-oldrelOK131
wasm-releaseOK181

Exports:animate2ddoadJunker2014downloadJunker2014estimate3dExpressionsextractGeneListfindAxialGenesgetReconstructedResultimageViewermaskerplot1dAllExpressionplot1dExpressionplotLossFunctiontoDataFrame

Dependencies:animationaskpassbase64encBiocFileCachebitbit64blobbslibcachemclicliprcommonmarkcpp11crayoncrosstalkcurldata.tableDBIdbplyrdigestdplyrevaluatefarverfastmapfilelockfontawesomefsgenericsggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2isobandjquerylibjsonliteknitrlabelinglaterlazyevallifecyclemagickmagrittrmemoisemimeopensslotelpillarpkgconfigplotlyprettyunitsprogresspromisespurrrR6rappdirsRColorBrewerRcppreadrrlangrmarkdownRSQLiteS7sassscalesshinysourcetoolsstringistringrsystibbletidyrtidyselecttinytextzdbutf8vctrsviridisLitevroomwithrxfunxtableyaml

R Package for Analyzing Tomo-seq Data

Ryosuke Matsuzawa

Rendered fromtomoseqr.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2022-10-24
Started: 2022-02-27