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.
Release Highlights in Current Stable¶
1.4.4 October 22, 2021¶
Use PegasusIO v0.4.0+ for data manipulation.
calculate_z_scorefunction to calculate standardized z-scored count matrix.
1.4.3 July 25, 2021¶
run_harmonyfunction to use GPU for computation.
1.4.2 July 19, 2021¶
Bug fix for
1.4.1 July 17, 2021¶
Add NMF-related options to
Add word cloud graph plotting feature to
pegasus aggregate_matrixcommand now allow sample-specific filtration with parameters set in the input CSV-format sample sheet.
Update doublet detection method:
1.4.0 June 24, 2021¶
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. (
Update mouse brain cell markers (
annotatefunction now adds annotation as a categorical variable and sort categories in natural order.
find_outlier_clustersfunction 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:
scatterfunction now plots all cells if
fix_cornersoption to fix the four corners when only a subset of cells is shown.
Fix a bug in
Fix bugs in functions
Support umap-learn v0.5+. (
Update doublet detection algorithm. (
Improve message reporting execution time spent each step. (Pegasus command line tool)