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MOCHA 1.1.0

• 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

• Addressed check errors in “donttest” examples.

MOCHA 1.0.1

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

MOCHA 1.0.0

• 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

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

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.