Package: tomoseqr 1.11.0

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]

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tomoseqr.pdf |tomoseqr.html✨
tomoseqr/json (API)
NEWS

# Install 'tomoseqr' in R:
install.packages('tomoseqr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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-1.11.0(bioc 3.21)tomoseqr-1.10.0(bioc 3.20)

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

geneexpressionsequencingrnaseqtranscriptomicsspatialvisualizationsoftware

4.18 score 15 scripts 131 downloads 13 exports 94 dependencies

Last updated 23 days agofrom:d515f3f531. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 18 2024
R-4.5-winOKNov 18 2024
R-4.5-linuxOKNov 18 2024
R-4.4-winOKNov 18 2024
R-4.4-macOKNov 18 2024
R-4.3-winOKNov 18 2024
R-4.3-macOKNov 18 2024

Exports:animate2ddoadJunker2014downloadJunker2014estimate3dExpressionsextractGeneListfindAxialGenesgetReconstructedResultimageViewermaskerplot1dAllExpressionplot1dExpressionplotLossFunctiontoDataFrame

Dependencies:animationaskpassbase64encBiocFileCachebitbit64blobbslibcachemclicliprcolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDBIdbplyrdigestdplyrevaluatefansifarverfastmapfilelockfontawesomefsgenericsggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttpuvhttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclemagickmagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplotlyprettyunitsprogresspromisespurrrR6rappdirsRColorBrewerRcppreadrrlangrmarkdownRSQLitesassscalesshinysourcetoolsstringistringrsystibbletidyrtidyselecttinytextzdbutf8vctrsviridisLitevroomwithrxfunxtableyaml

R Package for Analyzing Tomo-seq Data

Ryosuke Matsuzawa

Rendered fromtomoseqr.Rmdusingknitr::rmarkdownon Nov 18 2024.

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