Package: tomoda 1.17.0

Wendao Liu

tomoda: Tomo-seq data analysis

This package provides many easy-to-use methods to analyze and visualize tomo-seq data. The tomo-seq technique is based on cryosectioning of tissue and performing RNA-seq on consecutive sections. (Reference: Kruse F, Junker JP, van Oudenaarden A, Bakkers J. Tomo-seq: A method to obtain genome-wide expression data with spatial resolution. Methods Cell Biol. 2016;135:299-307. doi:10.1016/bs.mcb.2016.01.006) The main purpose of the package is to find zones with similar transcriptional profiles and spatially expressed genes in a tomo-seq sample. Several visulization functions are available to create easy-to-modify plots.

Authors:Wendao Liu [aut, cre]

tomoda_1.17.0.tar.gz
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tomoda.pdf |tomoda.html
tomoda/json (API)
NEWS

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

Bug tracker:https://github.com/liuwd15/tomoda/issues

Datasets:
  • zh.data - A raw read count matrix of zebrafish injured heart.

On BioConductor:tomoda-1.17.0(bioc 3.21)tomoda-1.16.0(bioc 3.20)

geneexpressionsequencingrnaseqtranscriptomicsspatialclusteringvisualization

4.00 score 2 scripts 234 downloads 18 exports 69 dependencies

Last updated 4 months agofrom:dcf5dcb1a9. Checks:7 OK, 1 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 15 2025
R-4.5-winOKFeb 15 2025
R-4.5-macWARNINGFeb 15 2025
R-4.5-linuxOKFeb 15 2025
R-4.4-winOKFeb 15 2025
R-4.4-macOKFeb 15 2025
R-4.3-winOKFeb 15 2025
R-4.3-macOKFeb 15 2025

Exports:corHeatmapcreateTomoembedPlotexpHeatmapfindPeakfindPeakGenegeneCorHeatmapgeneEmbedPlothierarchClustkmeansClustlinePlotnormalizeTomorunPCArunTSNErunUMAPscaleTomotomoMatrixtomoSummarizedExperiment

Dependencies:abindaskpassBiobaseBiocGenericsclicolorspacecrayoncurlDelayedArrayfansifarvergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelgluegtableherehttrIRangesisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigplyrpngR6rappdirsRColorBrewerRcppRcppEigenRcppTOMLreshape2reticulaterlangrprojrootRSpectraRtsneS4ArraysS4VectorsscalesSparseArraystringistringrSummarizedExperimentsystibbleUCSC.utilsumaputf8vctrsviridisLitewithrXVector

tomoda for tomo-seq data analysis

Rendered fromtomoda.Rmdusingknitr::rmarkdownon Feb 15 2025.

Last update: 2020-10-13
Started: 2020-09-14