v2.0.0 - Rome

What's Changed

• Small patch to fix release CI/CD tests by @ypriverol in #35
• feat: v1.0.0 — robustness, DDA support, new params, InfinDIA, docs by @ypriverol in #32
• Support multiplexing by @yueqixuan in #37
• Update the quantms-utils and pmultiqc images by @yueqixuan in #46
• Fix/insilico log diann 2.3.2 by @ypriverol in #40
• feat: rename FDR params and expose matrix-level q-value controls by @ypriverol in #44
• feat: add DIA-NN scoring mode parameter (Generic/Proteoforms/Peptidoforms) by @ypriverol in #45
• refactor: centralize blocked flags + fix missing guards from PR #36 review by @ypriverol in #48
• chore: bump version to 2.0.0 (Rome) and update CHANGELOG by @ypriverol in #50
• Minor update by @yueqixuan in #52
• feat: add DIA-NN 2.5.0 support with model fine-tuning documentation by @ypriverol in #53
• feat: add optional FINE_TUNE_MODELS step for DL model fine-tuning by @ypriverol in #54
• fix by @yueqixuan in #56
• fix by @yueqixuan in #57
• New release 2.0.0 including dda workflow for quantmsdiann by @ypriverol in #36
• chore: update CHANGELOG for 2.0.0 and remove mkdocs/ by @ypriverol in #58
• Release 2.0.0 by @ypriverol in #59
• docs: add container building and HPC deployment guide by @ypriverol in #60
• Dev by @ypriverol in #61

Full Changelog: v1.0.0...v2.0.0

v1.0.0 - Cambridge

What's Changed

• extract DIA-NN workflow from quantms by @yueqixuan in #11
• Add Peptidoform Scoring Control by @yueqixuan in #13
• small changes by @yueqixuan in #14
• Refactoring ongoing for quantmsdiann - iteration one Remove MSStats postprocessing by @ypriverol in #12
• Improving the workflow image by @ypriverol in #16
• Add Synchro-PASEF / timsTOF Flags by @yueqixuan in #18
• Minor update by @yueqixuan in #20
• Refactor: extract calibration params to meta by @yueqixuan in #22
• fix by @yueqixuan in #23
• Refactor empirical log parsing logic by @yueqixuan in #24
• Minor changes in the sdrf-pipelines by @ypriverol in #19
• Minor updates by @yueqixuan in #28
• Minor update by @yueqixuan in #31
• Suppress protein inference warning in PRELIMINARY_ANALYSIS by @ypriverol in #29
• Add Bruker/timsTOF auto-calibration warning by @ypriverol in #30
• Remove unused logo by @yueqixuan in #33
• First release of quantmsdiann including new features previously no supported by @ypriverol in #27

New Contributors

• @yueqixuan made their first contribution in #11
• @ypriverol made their first contribution in #12

Full Changelog: https://github.com/bigbio/quantmsdiann/commits/v1.0.0