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.
Version 1.1.0 December 7, 2020¶
Improve doublet detection in Scrublet-like way using automatic threshold selection strategy:
mark_doublets. Remove Scrublet from dependency, and remove
Enhance performance of log-normalization (
log_norm) and signature score calculation (
pegasus clustercommand, add
--genomeoption to specify reference genome name for input data of
Update Regress out tutorial.
Improve plotting functions:
Version 1.0.0 September 22, 2020¶
zarrfile format to handle data, which has a better I/O performance in general.
Data are manipulated in Multi-modal structure in memory.
Support focus analysis on Unimodal data, and appending other Unimodal data to it. (
Calculate signature / gene module scores. (calc_signature_score)
Principal-Component-level regress out. (pc_regress_out)
Allow DE analysis with sample attribute as condition. (Set
conditionargument in de_analysis)
Use static plots to show results (see Plotting):
Provide static plots: composition plot, embedding plot (e.g. tSNE, UMAP, FLE, etc.), dot plot, feature plot, and volcano plot;
Add more gene-specific plots: dendrogram, heatmap, violin plot, quality-control violin, HVF plot.
No longer support
h5scfile format, which was the output format of
aggregate_matrixcommand in Pegasus version
In cell quality-control, default percent of mitochondrial genes is changed from 10.0 to 20.0. (
percent_mitoargument in qc_metrics;
Move gene quality-control out of
filter_datafunction to be a separate step. (identify_robust_genes)
DE analysis now uses MWU test by default, not t test. (de_analysis)
infer_cell_types uses MWU test as the default
Speed up MWU test in DE analysis, which is inspired by Presto.
Integrate Fisher’s exact test via Cython in DE analysis to improve speed.
Version 0.17.2 June 26, 2020¶
Make Pegasus compatible with umap-learn v0.4+.
Use louvain 0.7+ for Louvain clustering.
Version 0.17.1 April 6, 2020¶
Improve pegasus command-line tool log.
Add human lung markers.
Improve log-normalization speed.
Provide robust version of PCA calculation as an option.
Add signature score calculation API.
Version 0.17.0 March 10, 2020¶
Support anndata 0.7 and pandas 1.0.
loomformat output writing function.
Bug fix on
mtxformat output writing function.
Update human immune cell markers.
Version 0.16.11 February 28, 2020¶
--subset-singletsoptions to ‘cluster’ command.
loomfile with user-specified batch key and black list.
Version 0.16.9 February 17, 2020¶
h5ad file with user-specified batch key.
Version 0.16.8 January 30, 2020¶
Allow input annotated
Version 0.16.7 January 28, 2020¶
mtx files of more filename formats.
Version 0.16.5 January 23, 2020¶
Add Harmony algorithm for data integration.
Version 0.16.3 December 17, 2019¶
Add support for loading mtx files generated from BUStools.
Version 0.16.2 December 8, 2019¶
Fix bug in ‘subcluster’ command.
Version 0.16.1 December 4, 2019¶
Fix one bug in clustering pipeline.
Version 0.16.0 December 3, 2019¶
Change options in ‘aggregate_matrix’ command: remove ‘–google-cloud’, add ‘–default-reference’.
Fix bug in ‘–annotation’ option of ‘annotate_cluster’ command.
Fix bug in ‘net_fle’ function with 3-dimension coordinates.
Use fisher package version 0.1.9 or above, as modifications in our forked fisher-modified package has been merged into it.
Version 0.15.0 October 2, 2019¶
Rename package to PegasusPy, with module name pegasus.
Version 0.14.0 September 17, 2019¶
Provide Python API for interactive analysis.
Version 0.10.0 January 31, 2019¶
Added ‘find_markers’ command to find markers using LightGBM.
Improved file loading speed and enabled the parsing of channels from barcode strings for cellranger aggregated h5 files.
Version 0.9.0 January 17, 2019¶
In ‘cluster’ command, changed ‘–output-seurat-compatible’ to ‘–make-output-seurat-compatible’. Do not generate output_name.seurat.h5ad. Instead, output_name.h5ad should be able to convert to a Seurat object directly. In the seurat object, raw.data slot refers to the filtered count data, data slot refers to the log-normalized expression data, and scale.data refers to the variable-gene-selected, scaled data.
In ‘cluster’ command, added ‘–min-umis’ and ‘–max-umis’ options to filter cells based on UMI counts.
In ‘cluster’ command, ‘–output-filtration-results’ option does not require a spreadsheet name anymore. In addition, added more statistics such as median number of genes per cell in the spreadsheet.
In ‘cluster’ command, added ‘–plot-filtration-results’ and ‘–plot-filtration-figsize’ to support plotting filtration results. Improved documentation on ‘cluster command’ outputs.
Added ‘parquet’ command to transfer h5ad file into a parquet file for web-based interactive visualization.
Version 0.8.0 November 26, 2018¶
Added support for checking index collision for CITE-Seq/hashing experiments.
Version 0.7.0 October 26, 2018¶
Added support for CITE-Seq analysis.
Version 0.6.0 October 23, 2018¶
Renamed scrtools to scCloud.
Added demuxEM module for cell/nuclei-hashing.
Version 0.5.0 August 21, 2018¶
Fixed a problem related AnnData.
Added support for BigQuery.
Version 0.4.0 August 2, 2018¶
Added mouse brain markers.
Allow aggregate matrix to take ‘Sample’ as attribute.
Version 0.3.0 June 26, 2018¶
scrtools supports fast preprocessing, batch-correction, dimension reduction, graph-based clustering, diffusion maps, force-directed layouts, and differential expression analysis, annotate clusters, and plottings.