NEWS

---

MOCHA 1.1.0 (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 (2023-12-21)

• Addressed check errors in "donttest" examples.

MOCHA 1.0.1 (2023-11-14)

• Deprecates testCoAccessibilityChromVAR() and testCoAccessibilityRandom() in favor of testCoAccessibility()
• Updates maintainer email

MOCHA 1.0.0 (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 (2022-12-06)

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