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v0.10 - #29

Merged

csoneson merged 66 commits into

mainfrom

v0.10

Aug 3, 2026

Merged

v0.10#29
csoneson merged 66 commits into
mainfrom
v0.10

Commits on Oct 31, 2025
- Version bump
  csoneson
  committed
  88346f5
- Define new filterFeaturesSE function, replacing tool-specific filtering functions
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  602b022
- Adapt unit tests to use new filterFeaturesSE function
  csoneson
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  ba6d957
- Add filtersDF argument to importDIANN, allow importing parquet files
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  823957c
- Add filtersDF argument to importSpectronaut
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  df1a186
- Add duckplyr to Suggests
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  c6b7a25
- Update NAMESPACE
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  dd6e85f
- Add default DF filter for DIA-NN
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  6fe21ff
- Add test for importDIANN with filtering
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  87fb10d
- Remove old filtering arguments in .check* functions, add checks for new filtering functions
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  0338653
- Update default filters to match previous defaults
  csoneson
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  9ed574d
- Swap filtering arguments in run*() functions
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  eaa9482
- Update filtering step in Rmd template
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  bc2d928
- Add test for no filtering
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  df905d4
- Update tests
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  033b872
- Update NEWS
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  6f7d923
- Add p-value histograms to pdfs with test result plots
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  6fee918
- Capture MSBooster information in readFragPipeInfo
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  5edde4d
Commits on Nov 1, 2025
- Bug fixes to p-value histogram plotting
  csoneson
  committed
  9f81299
Commits on Nov 3, 2025
- Add dependency on R >= 4.1 (pipe)
  csoneson
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  56dfeab
- Allow parquet format for DIANN also in argument checking
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  c5f426e
- Properly handle situation where DIANN log file is NULL
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  568b306
Commits on Dec 8, 2025
- Ignore 'iBAQ.peptides' column if present
  csoneson
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  8a9e146
- Update unit tests (ggplot2 changes)
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  17955c0
Commits on Jan 22, 2026
- Add genes, Protein.Names and Protein.Ids columns to DIA-NN import (assays and rowData columns)
  csoneson
  committed
  658a23a
Commits on Jan 23, 2026
- Fix filtering in importDIANN for large parquet files and add missing imports
  csoneson
  committed
  e5eafbd
Commits on Feb 13, 2026
- Bump version
  csoneson
  committed
  6dd6b4d
- Add runSEAnalysis function
  csoneson
  committed
  8723b7e
- Adapt functions to allow 'SE' expType
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  committed
  1975c3e
Commits on Feb 21, 2026
- Set default labelCol to idCol, filtersSE = list() in runSEAnalysis()
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  4c07cfa
- Check that default assay is a matrix
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  c8ef25f
- Generate test SE object
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  committed
  55da788
- Reoxygenize
  csoneson
  committed
  54cb1c3
- Add tests for checkArgumentsSE and runSEAnalysis
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  committed
  caa9645
Commits on Mar 6, 2026
- Use arrow instead of duckplyr to read parquet files
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  4f15a82
Commits on Mar 12, 2026
- Accommodate name change of msigdbdf to msigdbrdata
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  committed
  0fcd728
Commits on Mar 16, 2026
- Protect against all abundances in barplot of significant features being NA (could happen if labelFeaturesInVolcano is given)
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  a18a6fc
Commits on Apr 12, 2026
- Allow PEP.Quantity as iColPattern
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  82cf1d2
- Add clusterRows argument to makeAbundanceHeatmap
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  529ff78
- Add "sorted" settings to plotMissingValuesHeatmap
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  85cad32
- Update analysis template to only cluster heatmaps if the number of features is <= 10000
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  debb0af
Commits on Apr 26, 2026
- Add valueType argument to plotFractionDetectedPerSample, specify "percentage" in basic report
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  175d9e8
- Update documentation
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  42d00d3
Commits on Apr 29, 2026
- fix exclusion of se.logFC columns in prepareFinalSCE
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  10c5b1b
- exclude some lines from coverage calculations
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  de8efe3
- Add assertions in text snippet functions
  csoneson
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  0e3bc7e
- Expand unit tests
  csoneson
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  814c3f2
- Add Spectronaut example data
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  72683c0
- Add tests for Spectronaut functions
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  e9b24c9
Commits on Jun 10, 2026
- Update .Rbuildignore
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  47207e7
- Limit supported normalization methods in workflows
  csoneson
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  d837433
- Adapt to roxygen 8.0.0
  csoneson
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  7c5173e
- Fix tests
  csoneson
  committed
  83562df
Commits on Jun 23, 2026
- Bump version (0.10.2)
  csoneson
  committed
  241a1be
Commits on Jun 28, 2026
Commits on Jul 24, 2026
- Expand documentation
  csoneson
  committed
  3cc49a3
Commits on Jul 26, 2026
- Implement diff.mean.shared and diff.median.shared normalization options
  csoneson
  committed
  ab03f14
Commits on Aug 2, 2026
- Fix typo, rerender documentation
  csoneson
  committed
  2c97869
- Update docker image in GHA
  csoneson
  committed
  e7ed72b
- Increase tolerance in unit test to accommodate arm differences
  csoneson
  committed
  5806228
- Fix check note
  csoneson
  committed
  6211287
- Update actions
  csoneson
  committed
  06e533d

Commits

Commits on Oct 31, 2025

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Commits on Apr 29, 2026

Commits on Jun 10, 2026

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Commits on Aug 2, 2026