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

1.7.1 July 29, 2022

• Make command-line tool and API work with PegasusIO v0.7.0.

• Rename function arcsinh_transform to arcsinh, and allow set a user-specified count matrix for the transformation.

• Add functions log1p and normalize for preprocessing the count matrix.

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.

Improvement

• 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.

• Function scatter can plot multiple components and bases.