Pegasus for Single Cell Analysis

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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

1.9.0 January 19, 2024

New Feature and Improvement

  • calculate_z_score works with sparse count matrix. [PR 276 Thanks to Jayaram Kancherla]

  • Plotting functions (scatter, dotplot, violin, heatmap) now give warnings on genes/attributes not existing in the data, and skip them in the plots.

  • Improve heatmap:

    • Add show_sample_name parameter for cases of pseudo-bulk data, nanoString DSP data, etc.

    • Use Scipy’s linkage (scipy.cluster.hierarchy.linkage) for dendrograms to use its optimal ordering feature for better results (see groupby_optimal_ordering parameter).

  • Update human lung and mouse immune markers used by infer_cell_types function.

  • run_harmony can accept multiple attributes to be the batch key, by providing a list of attribute names to its batch parameter.

  • Expose online_batch_size parameter in nmf and integrative_nmf functions.