# Utilities for scRNA-seq data analysis

## Documentation for package ‘hammers’ version 1.0.0

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

## Help Pages

addCategory | Add a categorical column to a data frame based on another column
addMetadataCategory | Add a categorical column to a Seurat metadata or SingleCellExperiment coldata
addNormSilhouette | Adds normalized silhouette column to a single-cell expression object
centerOfMass | Calculate the center of mass of columns
checkGenes | Check if all genes exist in the single-cell expression object
colCenters | Calculate the centers of mass of metadata/coldata columns
colsDimPlot | Create a single-cell dimensionality reduction plot with added labeled points for numeric columns
computeSilhouette | Compute cluster silhouette for single-cell expression object
devPlot | Saves plot or list of plots
devPlot.default | Saves plot or list of plots
devPlot.function | Saves plot or list of plots
devPlot.ggplot | Saves plot or list of plots
devPlot.list | Saves plot or list of plots
distributionPlot | Plot the distribution of cells across two columns
findRareGenes | Find rare genes in a Seurat or SingleCellExpression object
geneCellSets | Generates cell sets for each input gene
geneCenters | Calculate the centers of mass of the expression of input genes
genePresence | Extract gene presence from a Seurat or SingleCellExperiment object
genesDimPlot | Create a single-cell dimensionality reduction plot with added labeled points for genes
joinCharCombs | Join all combinations of elements from character vectors
keyvalMap | Create a map from keys to values
normalizeSilhouette | Normalize silhouette by identity class for single-cell expression object
pointsDimPlot | Create a single-cell dimensionality reduction plot with added labeled points
prepAlluvial | Prepare dataframe for alluvial plot
pvalRiverPlot | Plot representation data frame
removeRareGenes | Remove rare genes from a Seurat or SingleCellExpression object
repAnalysis | Find the differential representation of two Seurat or SingleCellExperiment columns
safeMessage | Message an input if verbose is set to TRUE
safeMinmax | Perform min-max normalization when possible; otherwise return a single-value vector.