All pull requests

Pull requests

• Carry a pooled reference channel or file from an SDRF, never refuse it, and keep it out of every comparison

  ready for reviewready-for-agent
  #1508·trishorts opened Oct 26, 2026Contributor·

  ·
  3

• Draw each MBR random-RT decoy by rendezvous hashing, so unrelated donor peptides no longer re-draw it (#1484, cause 1)

  ready for reviewready-for-agent
  #1507·trishorts opened Oct 26, 2026Contributor·

  ·
  1

• Read a frozen hypothesis file and find each member's protein group (SETTEST1 S1: DEF-DIFF-SET input and members)

  ready for reviewready-for-agent
  #1506·trishorts opened Oct 26, 2026Contributor·

  ·
  1

• Move to TopDownProteomics 0.0.301, and read stacked terminal and labile ProForma modifications whole

  ready for reviewready-for-agent
  #1505·trishorts opened Oct 26, 2026Contributor·

  ·
  1

• Quantify a match ambiguous only in where its modifications sit (LocalizationAmbiguousPeptide)

  ready for reviewready-for-agent
  #1504·trishorts opened Oct 25, 2026Contributor·

  ·
  1

• Fragment co-elution against the best fragment, with candidate apexes and per-scan apex scores (FragmentCoElution, #1386 follow-up)

  ready for reviewready-for-agent
  #1503·trishorts opened Oct 25, 2026Contributor·

  ·
  1

• Classify the entrapment generator's truncationProductPeptide exclusion as Unpairable

  ready for reviewready-for-agent
  #1502·trishorts opened Oct 25, 2026Contributor·

  ·
  1

• Keep UniProt isoform scope: <molecule> on dbReference, and the entry's displayed isoform

  ready for reviewready-for-agent
  #1501·trishorts opened Oct 25, 2026Contributor·

  ·
  1

• Set aside iRT calibration anchors in near-empty stretches of the run (IrtCalibrationOptions.MinimumBinShare)

  ready for reviewready-for-agent
  #1500·trishorts opened Oct 25, 2026Contributor·

  ·
  1

• Robust option for NestedMixedModel: msqrob2 weights to convergence (STAT1 M3b)

  ready for reviewready-for-agent
  #1499·trishorts opened Oct 25, 2026Contributor·

  ·
  1

• Describe ModeratedContrast for the mixed model too, not only the linear model

  ready for reviewready-for-agent
  #1498·trishorts opened Oct 25, 2026Contributor·

  ·
  1

• Store GO annotation once per database, not once per search (per-database tables, member resolution, readers)

  ready for reviewready-for-agent
  #1497·trishorts opened Oct 25, 2026Contributor·

  ·
  1

• Quantify a protein whose peptides are each seen in only one, different sample

  ready for reviewready-for-agent
  #1486·trishorts opened Oct 20, 2026Contributor·

  ·
  3

• SDRF drafter: read a deposit's own design tables (Spectronaut, MSstats, MaxQuant) for conditions, replicates, fractions and samples

  ready for reviewready-for-agent
  #1483·trishorts opened Oct 18, 2026Contributor·

  ·
  1

• SDRF drafter: draft from any repository's record (SdrfDepositRecord), so a MassIVE draft names MassIVE, not PRIDE

  ready for reviewready-for-agent
  #1482·trishorts opened Oct 18, 2026Contributor·

  ·
  1

• PRIDE: keep a stopped download so the next call carries on, and resume one with no validator when its MD5 is checked

  ready for reviewready-for-agent
  #1481·trishorts opened Oct 18, 2026Contributor·

  ·
  1

• Add SpectralLibraryGenerator for predicted peptide libraries

  #1480·pcruzparri opened Oct 16, 2026Contributor·

  ·
  1

• Faster spectra-file I/O, spectral averaging, FlashLFQ and digestion, with identical results

  ready for reviewready-for-agent
  #1479·trishorts opened Oct 16, 2026Contributor·

  ·
  4

• Close a .parquet file that DIA-NN detection or loading refuses

  ready for reviewready-for-agent
  #1478·trishorts opened Oct 15, 2026Contributor·

  ·
  10

• Generate the statistics report (StatisticalReport.md) with SVG diagnostics, from the DEF-DIFF metadata and rows (STAT1 M6)

  ready for reviewready-for-agent
  #1475·trishorts opened Oct 15, 2026Contributor·

  ·
  1

• Write the prediction model names to the msp comment line

  #1473·pcruzparri opened Oct 14, 2026Contributor·

  ·
  1

• feat(statistics): a random-intercept model whose samples are measured on a latent scale or counted through it

  ready for reviewready-for-agent
  #1469·trishorts opened Oct 12, 2026Contributor·

  ·
  1

• feat(ptmqtl): one-form cells enter co-varying pairs as tied bounds, with a run covariate

  ready for reviewready-for-agent
  #1468·trishorts opened Oct 12, 2026Contributor·

  ·
  3

• Neural-network ensemble for target-decoy rescoring, with a pooled confident training sample (StatisticalModels)

  #1456·trishorts opened Oct 8, 2026Contributor·

  ·
  1

• Keep ValidatedFullSequence in the input's format and serialize the Koina payload at request time

  #1445·pcruzparri opened Oct 7, 2026Contributor·

  ·
  1