# Tool for Evaluation of Cell Identity from Transcription Profiles

## Documentation for package ‘CellScore’ version 1.22.0

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

## Help Pages

BarplotOnOff | Pyramid barplot of on/off scores
BoxplotCellScore | Boxplot of the CellScore values across test samples
CellScore | CellScore evaluates the identity of cells undergoing cell type transition
CellScoreReport | Generate a CellScore report
CosineSimScore | Cosine similarity score
extractTransitions | Extract scores for given cell transitions
heatmapOnOffMarkers | heatmapOnOffMarkers
OnOff | On/off score
PcaStandards | PCA plot on the most variable portion of the standard expression dataset
PlotCosineSimHeatmap | Plot heatmap of the cosine similarity score
RugplotCellScore | RugplotCellScore
rugplotDonorTargetTest | rugplotDonorTargetTest
ScatterplotCellScoreComponents | Scatterplot of the the donor-like and target-like scores
scatterplotDonorTargetTest | scatterplotDonorTargetTest