scikit-bio / scikit-bio

scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

https://scikit.bio

scikit-bio/scikit-bio Issues

qemu::aarch64-centos error
Closed 5 days ago
No wheel for python 3.12 / compilation fails on Python 3.12
Closed 7 days ago3
Slow unit test with `_enan.py`
Updated 9 days ago
dtype issues on Windows
Closed 9 days ago1
Issues with `SampleMetadata` read/write in Windows
Closed 9 days ago1
Feature: pLM-BLAST in scikit-bio
Updated 11 days ago8
FDR correction using statsmodels
Closed 11 days ago2
skbio.Table.write does not work as expected
Updated 12 days ago9
Pandas apply behavior not consistent across axes with compositional transforms
Updated 13 days ago1
Alpha Diversity indices produce zeros where previously undefined (NaN)
Closed 16 days ago18
NumPy 2.0 compatibility
Closed 19 days ago16
The IO registry sniffer is being used unexpectedly, and it is very expensive
Updated 17 days ago
FilePathSource can't handle POSIX paths
Updated 18 days ago
'import skbio.io' fails: ImportError: cannot import name 'Hashable' from 'collections' (/usr/local/lib/python3.11/collections/__init__.py)
Closed 18 days ago
SampleMetadata should be available at the module level
Updated 19 days ago
Differential abundance analysis via Dirichlet Multinomial
Closed 4 months ago2
Confusion between Ids and sequence in `Embedding` and `SequenceEmbedding`
Updated 25 days ago2
Add "taxonomy lineage" file format
Updated a month ago
Eigenvalues in RDA results
Updated a month ago
Protein LLM data structures
Closed a month ago19
Rename DistanceMatrix and OrdinationResults IDs
Updated 2 months ago1
TEST: Exception handling in skbio.io.format lacks test coverage
Updated 2 months ago
Support for stdin for at least FASTA/FASTQ
Updated 2 months ago1
DOC : default_write_format is not documented
Updated 2 months ago
Creating a hdf5-specific sniffer
Updated 2 months ago
Bioconda release
Updated 2 months ago
Compression differences on Windows
Updated 2 months ago
TreeNode.from_taxonomy should take a pandas dataframe as input
Updated 3 months ago1
Expose _vectorize_counts_and_tree
Updated 3 months ago
Efficient sequence alignment path data structure
Updated 3 months ago1
Review existing dependencies
Updated 3 months ago3
Top-level module `feature_table` should be added to documentation
Closed 3 months ago2
Intermediate BIOM file left after test
Closed 3 months ago
hdmedians is not available from conda-forge for windows
Closed 3 months ago5
Testing skbio against QIIME 2 to ensure integrity and/or identify breaking points
Updated 3 months ago
Pathlib support for the IO registry
Updated 4 months ago
Add more zero replacement methods
Updated 4 months ago1
Tokenizer compatibility with existing aligners / language models
Closed 4 months ago
EventMetadata as a new metadata format
Updated 4 months ago
OrdinationResults formatting assumes pd.Series on certain attributes
Updated 4 months ago
List of skbio changes that might affect QIIME 2
Updated 4 months ago
Update makefile
Updated 4 months ago
scikit-bio ASCII art should be updated
Updated 4 months ago
Streamlining requirements
Updated 4 months ago
Ignore Cython-derived .c files
Closed 4 months ago1
Add coverage to CI?
Closed 4 months ago3
Edge case: IO registry is not closing context correctly at program exit
Updated 5 months ago
Broken link in `diversity.alpha.simpson_e` docstring
Closed 5 months ago8
Replacing HTTPretty for unit test
Closed 5 months ago
Failing doctests for TabularMSA.loc and skbio.io.format.stockholm on Python 3.12
Closed 5 months ago