# R Package for Analyzing Tomo-seq Data

## Documentation for package ‘tomoseqr’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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.