Utilities for scRNA-seq data analysis

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Documentation for package ‘hammers’ version 0.99.11

• 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.