Pegasus for Single Cell Analysis

Pegasus is a tool for analyzing transcriptomes of millions of single cells. It is a command line tool, a python package and a base for Cloud-based analysis workflows.

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Release Highlights in Current Stable

1.7.0 July 5, 2022

New Features

• Add pegasus.elbowplot function to generate elbowplot, with an automated suggestion on number of PCs to be selected based on random matrix theory ([Johnstone 2001] and [Shekhar 2022]).

• Add arcsinh_transform function for arcsinh transformation on the count matrix.

API Changes

• Function nearest_neighbors has additional argument n_comps to allow use part of the components from the source embedding for calculating the nearest neighbor graph.

• Add n_comps argument for run_harmony, tsne, umap, and fle (argument name is rep_ncomps) functions to allow select part of the components from the source embedding.