R Package for Analyzing Tomo-seq Data


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Documentation for package ‘tomoseqr’ version 1.8.0

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