# MOCHA 1.0.2

# 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.
