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

1.4.5 January 24, 2022

  • Make several dependencies optional to meet with different use cases.

  • Adjust to umap-learn v0.5.2 interface.

1.4.4 October 22, 2021

  • Use PegasusIO v0.4.0+ for data manipulation.

  • Add calculate_z_score function to calculate standardized z-scored count matrix.

1.4.3 July 25, 2021

  • Allow run_harmony function to use GPU for computation.

1.4.2 July 19, 2021

  • Bug fix for --output-h5ad and --citeseq options in pegasus cluster command.

1.4.1 July 17, 2021

  • Add NMF-related options to pegasus cluster command.

  • Add word cloud graph plotting feature to pegasus plot command.

  • pegasus aggregate_matrix command now allow sample-specific filtration with parameters set in the input CSV-format sample sheet.

  • Update doublet detection method: infer_doublets and mark_doublets functions.

  • Bug fix.

1.4.0 June 24, 2021

  • Add nmf and integrative_nmf functions to compute NMF and iNMF using nmf-torch package; integrative_nmf supports quantile normalization proposed in the LIGER papers ([Welch19], [Gao21]).

  • Change the parameter defaults of function qc_metrics: Now all defaults are None, meaning not performing any filtration on cell barcodes.

  • In Annotate Clusters API functions:

    • Improve human immune cell markers and auto cell type assignment for human immune cells. (infer_cell_types function)

    • Update mouse brain cell markers (infer_cell_types function)

    • annotate function now adds annotation as a categorical variable and sort categories in natural order.

  • Add find_outlier_clusters function to detect if any cluster is an outlier regarding one of the qc attributes (n_genes, n_counts, percent_mito) using MWU test.

  • In Plotting API functions:

    • scatter function now plots all cells if attrs == None; Add fix_corners option to fix the four corners when only a subset of cells is shown.

    • Fix a bug in heatmap plotting function.

  • Fix bugs in functions spectral_leiden and spectral_louvain.

  • Improvements:

    • Support umap-learn v0.5+. (umap and net_umap functions)

    • Update doublet detection algorithm. (infer_doublets function)

    • Improve message reporting execution time spent each step. (Pegasus command line tool)