8000 Commits · aertslab/pycisTopic · GitHub

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Commits

Commits on Apr 24, 2024

Update Polars syntax to 0.20.5+ version.
ghuls
committed

Commits on Apr 4, 2024

Add nucleosome signal statistics to fragments stats per CB dataframe.
ghuls
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Commits on Mar 19, 2024

Fix deprecation warnings from Polars 0.20.x in fragments.py and genomic_ranges.py.
ghuls
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Commits on Mar 14, 2024

Speedup load_word_topics by reading Mallet state file with Polars.
ghuls
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Add option to specify Mallet binary path in topic modeling CLI subcommand.
ghuls
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Display "True" and "False" option for "--keep" option in topic modeling CLI help.
ghuls
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Reformat cistopic_class.py with ruff and rearange imports.
ghuls
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Construct Mallet command lines as a list of arguments instead of relying on the shell.
ghuls
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Remove some unused variables and imports.
ghuls
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Commits on Mar 13, 2024

Commits on Mar 1, 2024

Fix get_tss_annotation_from_ensembl function so it works with Polars 0.20.x.
ghuls
committed

Commits on Feb 23, 2024

Add new module files to documentation and render numpy doc sections.
ghuls
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Commits on Jan 30, 2024

Do not use PyArrow when reading fragments file with Polars as it seems to deadlock sometimes.
ghuls
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Commits on Nov 29, 2023

Remove trailing dot(s) from the output prefix.
ghuls
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Commits on Nov 17, 2023

Do not skip first line When reading UCSC chrom sizes file and start column names line in chrom sizes and alias TSV file with a comment character.
ghuls
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Commits on Nov 15, 2023

Commits on Nov 8, 2023

Expose "get_ncbi_chrom_sizes_and_alias_mapping" and "get_ucsc_chrom_sizes_and_alias_mapping" in pycistopic CLI.
ghuls
committed

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