bb_triplecluster: A function to generate clusters from scRNA-seq data

In blaserlab/blaseRtools: R Tools for Blaser Lab Data Analysis

A function to generate clusters from scRNA-seq data

Description

Based on Monocle3's Partitions, Leiden, and Louvain clustering methods. Implemented mostly with default values. Seurat objects will be converted to cell_data_set objects for the clustering. The function produces a list of top markers for each cluster type and returns these assignments to the original object as new cell metadata columnts.

Usage

bb_triplecluster(
  obj,
  n_top_markers = 50,
  outfile = NULL,
  n_cores = 8,
  cds = NULL
)

Arguments

obj	A Seurat or cell_data_set object
n_top_markers	Number of top markers to identify per cell group, Default: 50
outfile	Name of a csv file to hold the top marker results. If null, will place "top_markers.csv" in the working directory, Default: NULL
n_cores	Number of processor cores to use, Default: 8
cds	Provided for backwards compatibility for existing code. If a value is supplied it will be transferred to obj and a warning message will be emitted, Default: NULL

Value

A modified Seurat or cell_data_set object

blaserlab/blaseRtools documentation built on April 14, 2025, 6:04 p.m.