PegasusIO for reading / writing single-cell genomics data¶
PegasusIO is the IO package for Pegasus.
Version 0.8.0 February 7, 2023¶
Version 0.7.1 August 7, 2022¶
Bug fix in
to_anndatafunction. [PR #97]
Version 0.7.0 July 25, 2022¶
The default count matrix of a
UnimodalDataobject now has key
Version 0.6.2 July 5, 2022¶
transposeoption to transpose the loaded count matrix. Only works for CSV or TSV-format files.
Version 0.6.1 May 18, 2022¶
Make the generated
h5format count matrix readable by
read10xCountfunction in R DropletUtil package. [PR #93]
Version 0.6.0 May 14, 2022¶
Version 0.5.1 February 10, 2022¶
Version 0.5.0 January 24, 2022¶
Add support on 10x Visium spatial data
Read the data folder by
Write 10x Visium data to Zarr format by
write_outputfunction with output file name of
Version 0.4.1 November 4, 2021¶
Fix issues on
Version 0.4.0 October 19, 2021¶
varpfields to store graph representation in terms of square matrices.
Allow copy from View of
register_attrfunction to register an attribute of a specified type in
obsmfields. This can be useful for adding information like gene signatures, etc.
Version 0.3.1 July 16, 2021¶
aggregate_matricesfunction, allow sample-specific filtration on minimum number of UMIs (
nUMIcolumn in sample sheet) and minimum number of genes (
nGenecolumn in sample sheet), which would overwrite the corresponding parameters of the function for these samples.
Version 0.3.0 July 6, 2021¶
Add support for composite list (e.g.
[0, pd.DataFrame, np.ndarray]) in
data.unsfield for Zarr read/write.
Version 0.2.14 June 28, 2021¶
filter_datafunction to keep QC statistics if needed.
Version 0.2.13 June 24, 2021¶
aggregate_matricesfunction now accepts sample sheet in Python dictionary format besides a CSV file path string. See details in its description in API panel.
Version 0.2.12 May 28, 2021¶
Version 0.2.11 May 17, 2021¶
Version 0.2.10 February 2, 2021¶
Version 0.2.9 December 25, 2020¶
Fix a bug for caching percent mito rate.
Improve write_mtx function.
Version 0.2.8 December 7, 2020¶
Add support on loading
loomfile with Seurat-style cell barcode and feature key names.
Bug fix: resolve an issue on count matrix dimension inconsistency with feature metadata on data aggregation, when last feature has
0count across all cell barcodes. Thanks to Mikhail Alperovich for reporting this issue.
Other bug fix and performance improvements.
Version 0.2.7 October 13, 2020¶
Add support for Nanostring GeoMx data format.
Version 0.2.6 September 28, 2020¶
Fix bug in SCP compatible output generation.
Version 0.2.5 August 19, 2020¶
Adjustment for Pegasus command usage.
Version 0.2.2 June 16th, 2020¶
Fix bugs in data aggregation.
Version 0.2.1 June 8th, 2020¶
Fix bug in processing single
Version 0.2.0 June 7th, 2020¶