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Changelog

Source: NEWS.md

MOCHA 1.1.0

CRAN release: 2024-01-25

  • New Functions:

    • Sharing MOCHA objects between file systems
      • packMOCHA
      • unpackMOCHA
    • Exporting for genome browsers (bigwig, bigbed)
      • exportCoverage
      • exportDifferentials
      • exportMotifs
      • exportOpenTiles
      • exportSmoothedInsertions
    • Getters
      • getCellTypeTiles
      • getCellTypes
      • getPromoterGenes
      • getSampleCellTypeMetadata
    • Other
      • mergeTileResults
      • plotIntensityDistribution
      • renameCellTypes

  • Deprecated Functions:

    • runLMEM, pilotLMEM, runZIGLMM, pilotZIGLMM, IndividualZIGLMM, getModelValues, varZIGLMM, processModelOutputs

  • Updates test data to consistently use TxDb hg19 references.

  • Various minor bug and documentation fixes.

MOCHA 1.0.2

CRAN release: 2023-12-21

  • Addressed check errors in “donttest” examples.

MOCHA 1.0.1

CRAN release: 2023-11-14

MOCHA 1.0.0

CRAN release: 2023-06-12

  • Adopting semantic versioning starting with this version, versioning reflects breaking changes compared to previous CRAN release.
  • Includes test improvements
  • New functions bulkDimReduction, bulkUMAP, MotifEnrichment, MotifSetEnrichmentAnalysis, pilotLMEM, runLMEM, pilotZIGLMM, runZIGLMM, combineSampleTileMatrix, getCoverage
  • Improvements to metadata carried by output objects

MOCHA 0.2.5

  • patches a bug (rounding error) found in getDifferentialAccessibleTiles (#125), and reverts to using mclapply parallelization forgetDifferentialAccessibleTiles.
  • adds conditional tests (and snapshot tests) on the COVID dataset to ensure reproducibility with results in the MOCHA manuscript
  • updates the COVID vignette through differentials to reflect the latest usage.

MOCHA 0.2.4

  • Fixes bug in callOpenTiles where “Clusters” was hardcoded in the step computing fragment counts table.
  • Parallelization overhaul to address memory leaks when using parLapply. ParLapply is now passed a helper function directly and a single object input to that function, where the input object is a list containing all variables needed in the helper function.

MOCHA 0.2.3

  • MOCHA MultiAssayExperiment and MOCHA SummarizedExperiment objects now contain new metadata
  • CallOpenTiles now only only accepts the database package names (strings) for Genome, OrgDb, and TxDb, and not the in-memory R objects for those database packages
  • Downstream functions where Genome, OrgDb, and TxDb were previously inputs now check the input MOCHA object’s metadata to load the relevant databases.

MOCHA 0.2.2

  • getCoAccessibleLinks
  • testCoAccessibilityChromVar and testCoAccessibilityRandom
  • combineSampleTileMatrix

MOCHA 0.2.1

  • This release adds additional test coverage with new test data, covering edge cases in callOpenTiles.

  • Removes option log2Intensity from getSampleTileMatrix (done by default in getDifferentialAccessibleTiles)

MOCHA 0.2.0

  • This includes the initial release of package on CRAN, adds updated requirements for R >= 4.1.0 and plyranges >1.14.0

MOCHA 0.1.0

CRAN release: 2022-12-06

  • Added a NEWS.md file to track changes to the package.
  • MOCHA is submitted to CRAN as an initial release.