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¶
1.2.0 December 25, 2020¶
tSNE support:
tsne
function in API: Use FIt-SNE for tSNE embedding calculation. No longer support MulticoreTSNE.Determine
learning_rate
argument intsne
more dynamically. ([Belkina19], [Kobak19])By default, use PCA embedding for initialization in
tsne
. ([Kobak19])Remove
net_tsne
andfitsne
functions from API.Remove
--net-tsne
and--fitsne
options from pegasus cluster command.
Add multimodal support on RNA and CITE-Seq data back:
--citeseq
,--citeseq-umap
, and--citeseq-umap-exclude
in pegasus cluster command.Doublet detection:
Add automated doublet cutoff inference to
infer_doublets
function in API. ([Li20-2])Expose doublet detection to command-line tool:
--infer-doublets
,--expected-doublet-rate
, and--dbl-cluster-attr
in pegasus cluster command.Add doublet detection tutorial.
Allow multiple marker files used in cell type annotation:
annotate
function in API;--markers
option in pegasus annotate_cluster command.Rename pc_regress_out function in API to
regress_out
.Update the regress out tutorial.
Bug fix.