Reference

All functions
Antler-class	Interface of the Antler package (reference class).
add_color_map	Add a new color map.
brew_more_colors()	Build and name color palette vectors
build_pseudotime_tree	Reconstruct pseudotime tree
carve	Reconstruct cell state lineage trajectories
cell_clusters_identify	Cluster cells from a selected gene module list.
cell_names	Returns the current cell names.
cell_state_graph_plot	Plot cell state graph
convert_ensembl_id_to_name	Replace ensembl gene ids with gene names
define_cell_samples	Define the cells sample names and map the cell colors to some of their metadata.
dispersed_genes	Print highly-dispersed genes.
exclude_exotic_genes	Exclude genes from their name pattern.
exclude_unexpressed_genes	Exclude genes with low expression.
export_expressionset	Export internal expression set.
gene_modules_export	Save gene module to file.
gene_modules_identify	Identify gene modules.
gene_modules_report_genes	Report whether genes belong to modules
gene_modules_select_from_gene_names	Select gene modules from gene names
gene_modules_select_from_ids	Select gene modules from indices
gene_names	Returns the current gene names.
genes_from_GOterms()	Convert GO terms to gene names.
load_dataset	Import a RNA-seq dataset into Antler.
normalize	Normalize gene expression levels.
num_cells	Returns the current number of cells.
num_genes	Returns the current number of genes.
plot_QC	Render various plots indicating the tallied gene and cell count distributions.
plot_pseudotime_dynamics	Visualize the smoothed gene expression dynamics along specific branches of the pseudotime tree.
plot_transcriptome_summary	Heatmap of the transcriptomic profile.
read_counts	Returns a gene expression matrix.
remove_cells	Exclude cells from the current dataset
remove_clusters	Exclude cells belonging to one or more clusters
remove_genes	Exclude genes from the current dataset.
remove_outliers	Remove outlier genes and cells.
report	Print the current analysis log in the console.
sample_size	Returns a contingency table with the counts per type of cell samples.
save_dataset	Save dataset to file.
select_dispersed_genes	Select highly-dispersed genes.
set_favorite_genes	Store a list of favorite gene names.
smooth	Smooth gene expression using the cell state graph
test_kernel_widths	Plot cell state graph over different gaussian kernel widths