v1.2.3

What's Changed

• Upgrade to pandas 2.0 by @scottgigante in #137

Full Changelog: v1.2.2...v1.2.3.post2

v1.2.2

What's Changed

• Remove py36 by @scottgigante in #134
• Bump urllib by @scottgigante in #136

Full Changelog: v1.2.1...v1.2.2

v1.2.1

What's Changed

• Clear warnings and test errors by @scottgigante-immunai in #133

Full Changelog: v1.2.0...v1.2.1

scprep v1.2.0

What's Changed

• Print traceback on RFunction error by @scottgigante-immunai in #128
• Add ignore_nan arg to scprep.stats.pairwise_correlation by @scottgigante-immunai in #123

New Contributors

• @scottgigante-immunai made their first contribution in #128

Full Changelog: v1.1.0...v1.2.0

scprep v1.1.0

Changeset:

• Added scprep.run.DyngenSimulate
• Improved behavior of DREVI with constant inputs
• Added pre-commit for clearer development guidelines

scprep v1.0.1

Changeset:

• scprep.plot.histogram supports 0 and negative data with log='x' and log=True
• scprep.filter.filter_values (library_size, gene_set_expression) supports cutoff=(low, high) and percentile=(low, high)
• variable genes calculation is more stable using a rolling median (no longer uses loess)
• added scprep.measure.gene_capture_count
• added scprep.stats.t_statistic and scprep.stats.rank_sum_statistic
• scprep.stats.differential_expression supports measure='ttest' and measure='ranksum'

scprep v1.0

Changeset:

• upgraded pandas dependency from <0.24 to >0.25
• added scprep.run.Slingshot
• added scprep.stats.differential_expression
• added scprep.measure.gene_variability and select.highly_variable_genes
• added scprep.io.download submodule
• added scprep.io.save_mtx
• many bugfixes

scprep v0.12.1

Changeset:

• addition of scprep.plot.colors
• plot.marker_plot no longer fails with NaN input
• substantial refactor of ScatterParams
• various bugfixes

scprep v0.12.0

Changeset:

• added scprep.run.splatter, a Python port of the Bioconductor Splatter package
• added compatibility for Cellranger 3.0 10X files
• optional dependencies are now loaded at runtime
• scprep.plot.marker_plot now sorts markers and tissues by linkage by default
• bugfixes in multi-dataset histograms

scprep v0.11.0

Changeset:

• moved scprep.hdf5 to scprep.io.hdf5
• added scprep.plot.jitter
• added experimental alternative to fcsparser for malformed fcs files
• changed gene_set_expression to not library size normalize by default
• scprep.io.load_10X_zip now accepts urls
• added examples to docs for scatter plots and jitter plots
• scprep.plot.histogram, scprep.plot.plot_library_size and scprep.plot.plot_gene_set_expression now accept multiple datasets
• various bugfixes and improved testing