PegasusIO for reading / writing single-cell genomics data
PegasusIO is the IO package for Pegasus.
Version 0.9.1 June 11, 2024
The
copy
function ofMultimodalData
andUnimodalData
removes unused categories inobs_names
andvar_names
. [PR #114]
Version 0.9.0 January 19, 2024
UnimodalData’s copy function now returns a MultimodalData object by default. Use cases:
data[indices, :].copy()
returns a MultimodalData object;data[indices, :].copy(to_unidata=True)
still returns a UnimodalData object.
Version 0.8.2 January 5, 2024
Version 0.8.1 July 13, 2023
Bug fix and backward compatibility support
Version 0.8.0 February 7, 2023
Version 0.7.1 August 7, 2022
Bug fix in
to_anndata
function. [PR #97]
Version 0.7.0 July 25, 2022
The default count matrix of a
UnimodalData
object now has keycounts
instead ofX
.Add
uid
option toUnimodalData
constructor.Add
get_uid
function toUnimodalData
class.
Version 0.6.2 July 5, 2022
In
read_input
function, addtranspose
option to transpose the loaded count matrix. Only works for CSV or TSV-format files.
Version 0.6.1 May 18, 2022
Make the generated
h5
format count matrix readable byread10xCount
function 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
read_input
function withfile_type="visium"
option.Write 10x Visium data to Zarr format by
write_output
function with output file name of.zarr.zip
extension.
Version 0.4.1 November 4, 2021
Fix issues on
UnimodalData
object construction.
Version 0.4.0 October 19, 2021
Add
obsp
andvarp
fields to store graph representation in terms of square matrices.Allow copy from View of
AnnData
.In
MultimodalData
, addregister_attr
function to register an attribute of a specified type inobs
orobsm
fields. This can be useful for adding information like gene signatures, etc.
Version 0.3.1 July 16, 2021
For
aggregate_matrices
function, allow sample-specific filtration on minimum number of UMIs (nUMI
column in sample sheet) and minimum number of genes (nGene
column 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]
) indata.uns
field for Zarr read/write.
Version 0.2.14 June 28, 2021
Add parameter
uns_white_list
infilter_data
function to keep QC statistics if needed.
Version 0.2.13 June 24, 2021
The
aggregate_matrices
function 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
Bug fix.
Version 0.2.11 May 17, 2021
Bug fix.
Version 0.2.10 February 2, 2021
Feature enhancement.
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
loom
file 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
0
count 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.
Fix bugs.
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 h5
file.
Version 0.2.0 June 7th, 2020
Initial release.