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¶
1.5.0 March 9, 2022¶
New Features
Spatial data analysis:
Enable
pegasus.read_input
function to load 10x Visium data: setfile_type="visium"
option.Add
pegasus.spatial
function to generate spatial plot for 10x Visium data.Add Spatial Analysis Tutorial in Tutorials.
Pseudobulk analysis: see summary
Add
pegasus.pseudobulk
function to generate pseudobulk matrix.Add
pegasus.deseq2
function to perform pseudobulk differential expression (DE) analysis, which is a Python wrapper of DESeq2.Requires rpy2 and the original DESeq2 R package installed.
Add
pegasus.pseudo.markers
,pegasus.pseudo.write_results_to_excel
andpegasus.pseudo.volcano
functions for processing pseudobulk DE results.Add Pseudobulk Analysis Tutorial in Tutorials.
Add
pegasus.fgsea
function to perform Gene Set Enrichment Analysis (GSEA) on DE results and plotting, which is a Python wrapper of fgsea.Requires rpy2 and the original fgsea R package installed.
API Changes
Function
correct_batch
, which implements the L/S adjustment batch correction method, is obsolete. We recommend usingrun_harmony
instead, which is also the default of--correct-batch-effect
option inpegasus cluster
command.pegasus.highly_variable_features
allows specify custom attribute key for batches (batch
option), and thus removeconsider_batch
option. To select HVGs without considering batch effects, simply use the default, or equivalently usebatch=None
option.Add
dist
option topegasus.neighbors
function to allow use distance other than L2. (Contribution by hoondy in PR 233)Available options:
l2
for L2 (default),ip
for inner product, andcosine
for cosine similarity.
The kNN graph returned by
pegasus.neighbors
function is now stored inobsm
field of the data object, no longer inuns
field. Moreover, the kNN affinity matrix is stored inobsp
field.
Improvements
Adjust
pegasus.write_output
function to work with Zarr v2.11.0+.