Cell Type Pipes for Single-Cell RNA Sequencing Data


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Documentation for package ‘cellpypes’ version 0.1.3

Help Pages

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.
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