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.
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 inpegasus 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
andmark_doublets
functions.Bug fix.
1.4.0 June 24, 2021¶
Add
nmf
andintegrative_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 areNone
, 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 ifattrs
==None
; Addfix_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
andspectral_louvain
.Improvements:
Support umap-learn v0.5+. (
umap
andnet_umap
functions)Update doublet detection algorithm. (
infer_doublets
function)Improve message reporting execution time spent each step. (Pegasus command line tool)