v3.0.0

3.0.0 (2025-07-15)

⚠ BREAKING CHANGES

• allow to run spia on multiple pathway databases (separately) (#157)
• switch to fastp for trimming (#155) (f359daf)

Features

• allow to run spia on multiple pathway databases (separately) (#157) (57479fa)

Bug Fixes

• set spia mem_mb to 32G and threads to 32 (#154) (9964ecf)

v2.11.2

2.11.2 (2025-05-19)

Bug Fixes

• make isoformanalyzer annotation match transcriptome reference (#152) (0320826)

v2.11.1

2.11.1 (2025-04-24)

Bug Fixes

• Remove model filtering of logcount matrix (#144) (de347fa)

v2.11.0

2.11.0 (2025-04-23)

Features

• Add TPM matrix generation and integration into workflow (#146) (3c6bdac)

Bug Fixes

• make postprocess sorting work with more than one signed_pi value column (#150) (4b3417a)
• use verify_integrity=True in pandas set_index() for samples and units to check for duplicates (#149) (9657c75)

v2.10.0

2.10.0 (2025-03-19)

Features

• Enrichment and pathway scatter-plots (#136) (29684af)

Bug Fixes

• move summing of go-term fold changes out of log-space (#141) (66bed4a)

v2.9.0

2.9.0 (2025-03-11)

Features

• Make PCA plots interactive and switch to HTML format (#137) (d0e6e78)

Bug Fixes

• add support for drosophila melanogaster and other non-standard species (#142) (dedfdf7)
• Improve error handling for missing or empty column values in dataframe with duplicate definitions (#138) (7f3d590)

v2.8.4

2.8.4 (2024-12-18)

Bug Fixes

• handle NA values correctly in meta compare pathways (#134) (71778df)

v2.8.3

2.8.3 (2024-12-11)

Bug Fixes

• Update to latest datavzrd wrapper (#126) (8b57d60)
• use latest stable datavzrd, fixing a bug with numpy values in configs; increase default ensembl release version to 113 (112 currently has biomart issues) (#130) (b11f100)

v2.8.2

2.8.2 (2024-10-18)

Bug Fixes

• Convert pval and qval to heatmap (#123) (478c759)
• Move NA values to end of table (#124) (df807a5)
• Update max in memory rows for diffexp report (#122) (830e678)

Performance Improvements

• Update to latest datavzrd wrapper (#125) (3a4c020)
• Update to latest datavzrd wrapper version (#120) (7b2767c)

v2.8.1

2.8.1 (2024-09-20)

Performance Improvements

• Update datavzrd wrapper version (#118) (e498079)