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:
tomoda_1.17.0.tar.gz
tomoda_1.17.0.zip(r-4.5)tomoda_1.17.0.zip(r-4.4)tomoda_1.17.0.zip(r-4.3)
tomoda_1.17.0.tgz(r-4.5-any)tomoda_1.17.0.tgz(r-4.4-any)tomoda_1.17.0.tgz(r-4.3-any)
tomoda_1.17.0.tar.gz(r-4.5-noble)tomoda_1.17.0.tar.gz(r-4.4-noble)
tomoda_1.17.0.tgz(r-4.4-emscripten)tomoda_1.17.0.tgz(r-4.3-emscripten)
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
- 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
Last updated 4 months agofrom:dcf5dcb1a9. Checks:7 OK, 1 WARNING. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 15 2025 |
| R-4.5-win | OK | Feb 15 2025 |
| R-4.5-mac | WARNING | Feb 15 2025 |
| R-4.5-linux | OK | Feb 15 2025 |
| R-4.4-win | OK | Feb 15 2025 |
| R-4.4-mac | OK | Feb 15 2025 |
| R-4.3-win | OK | Feb 15 2025 |
| R-4.3-mac | OK | Feb 15 2025 |
Exports:corHeatmapcreateTomoembedPlotexpHeatmapfindPeakfindPeakGenegeneCorHeatmapgeneEmbedPlothierarchClustkmeansClustlinePlotnormalizeTomorunPCArunTSNErunUMAPscaleTomotomoMatrixtomoSummarizedExperiment
Dependencies:abindaskpassBiobaseBiocGenericsclicolorspacecrayoncurlDelayedArrayfansifarvergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelgluegtableherehttrIRangesisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigplyrpngR6rappdirsRColorBrewerRcppRcppEigenRcppTOMLreshape2reticulaterlangrprojrootRSpectraRtsneS4ArraysS4VectorsscalesSparseArraystringistringrSummarizedExperimentsystibbleUCSC.utilsumaputf8vctrsviridisLitewithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Correlation heatmap of sections | corHeatmap |
| Create an object representing tomo-seq data | createTomo createTomo,matrix-method createTomo,missing-method createTomo,SummarizedExperiment-method |
| Embedding plot for sections | embedPlot |
| Expression heatmap | expHeatmap |
| Find peak in a vector | findPeak |
| Find peak genes | findPeakGene |
| Correlation heatmap of genes | geneCorHeatmap |
| Embedding plot for genes | geneEmbedPlot |
| Hierarchical clustering across sections | hierarchClust |
| K-Means clustering across sections | kmeansClust |
| Line plot for expression traces | linePlot |
| Normalize data | normalizeTomo |
| Perform PCA | runPCA |
| Perform TSNE | runTSNE |
| Perform UMAP | runUMAP |
| Scale data | scaleTomo |
| Create an object from matrix | tomoMatrix |
| Create an object from SummarizedExperiment | tomoSummarizedExperiment |
| A raw read count matrix of zebrafish injured heart. | zh.data |