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✨
DESCRIPTION |NEWS
card.svg |card.png
tomoseqr/json (API)

# 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.

geneexpression sequencing rnaseq transcriptomics spatial visualization software

4.20 score 16 scripts 13 exports 88 dependencies

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

Target	Result	Time
bioc-checks	WARNING	196
linux-devel-x86_64	OK	226
source / vignettes	OK	242
linux-release-x86_64	OK	232
macos-release-arm64	OK	95
macos-oldrel-arm64	OK	95
windows-devel	OK	124
windows-release	OK	115
windows-oldrel	OK	121
wasm-release	OK	197

Exports:animate2d doadJunker2014 downloadJunker2014 estimate3dExpressions extractGeneList findAxialGenes getReconstructedResult imageViewer masker plot1dAllExpression plot1dExpression plotLossFunction toDataFrame

Dependencies:animation askpass base64enc BiocFileCache bit bit64 blob bslib cachem cli clipr commonmark cpp11 crayon crosstalk curl data.table DBI dbplyr digest dplyr evaluate farver fastmap filelock fontawesome fs generics ggplot2 glue gtable highr hms htmltools htmlwidgets httpuv httr httr2 isoband jquerylib jsonlite knitr labeling later lazyeval lifecycle magick magrittr memoise mime openssl otel pillar pkgconfig plotly prettyunits progress promises purrr R6 rappdirs RColorBrewer Rcpp readr rlang rmarkdown RSQLite S7 sass scales shiny sourcetools stringi stringr sys tibble tidyr tidyselect tinytex tzdb utf8 vctrs viridisLite vroom withr xfun xtable yaml

R Package for Analyzing Tomo-seq Data

Rendered fromtomoseqr.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Animate 2D expressions along one axis and generate GIF file.	animate2d
Load data of Junker2014 from cache.	doadJunker2014
Download part of the Tomo-seq data published by Junker et al.	downloadJunker2014
Estimate 3d expressions	estimate3dExpressions
Extract geneIDs to which hoge can be applied.	extractGeneList
Find peak genes on axial	findAxialGenes
Get reconstructed matrix	getReconstructedResult
Output the reconstructed expression pattern as an image.	imageViewer
A matrix containing mask data.	mask
Make mask	masker
Plot expressions of all genes along an axis	plot1dAllExpression
Plot expression of single gene along an axis	plot1dExpression
Plot the trend of the value of the loss function.	plotLossFunction
A data.frame object containing a simulated Tomo-seq data for x-axis sections.	testx
A data.frame object containing a simulated Tomo-seq data for y-axis sections.	testy
A data.frame object containing a simulated Tomo-seq data for z-axis sections.	testz
Convert reconstructed matrix to data.frame.	toDataFrame
A tomoSeq object.	tomoObj