Cell Type Pipes for Single-Cell RNA Sequencing Data

Documentation for package ‘cellpypes’ version 0.3.0

classify	Classify cells on previously defined rules
class_to_deseq2	Create DESeq2 object for a given cell type
feat	Feature plots: Color gene expression in 2D embeddings
find_knn	Find approximate k-nearest neighbors
is_classes	Check if obj$classes looks as expected. is_class returns FALSE for example in these cases: is_classes(NULL) is_classes(data.frame()) is_classes(data.frame(class=c("T","T"), parent=c("..root..","..root..")))
is_rules	Check if obj$rules looks as expected.
knn_refine	Refine cell type labels with knn classifier
plot_classes	Call and visualize 'classify' function
plot_last	Plot the last modified rule or class
pool_across_neighbors	Sum up x across neighbors in a nearest neighbor graph.
pseudobulk	Form pseudobulks from single cells.
pseudobulk_id	Generate unique IDs to identify your pseudobulks.
pype_code_template	Generate code template for cellpype rules
pype_from_seurat	Convert Seurat to cellpypes object.
rule	Add a cell type rule.
simulated_umis	Simulated scRNAseq data