<commit_before>## basejump 0.12.17 (2020-10-01)

### Major changes

- `Ensembl2Entrez`: Improved internal matching engine, to allow reverse matching
  of Entrez identifiers to Ensembl identifiers.
- Now exporting `Entrez2Ensembl`, which works like `Entrez2Ensembl`.
- New S4 class `Entrez2Ensembl`, which inherits `Ensembl2Entrez` structure.

### Minor changes

- `makeSummarizedExperiment`: No longer requiring primary `assay` defined to
  be named "counts". This isn't appropriate for `SummarizedExperiment` objects
  defined in the new DepMapAnalysis package.

## basejump 0.12.16 (2020-09-29)

### Minor changes

- `makeProtein2GeneFromEnsembl`: Improved error message on match failure. Now
  returns the protein IDs that failed to match more clearly.

## basejump 0.12.15 (2020-09-25)

### New classes

- `Protein2Gene`: `DataFrame` with `proteinID`, `geneID`, and `geneName`
  columns. Use corresponding `makeProtein2GeneFromEnsembl` to generate object
  simplify using Ensembl protein IDs as input.

### New functions

- `getEnsDb`: Now exporting function that was used internally to obtain `EnsDb`
  object from AnnotationHub.
- `makeProtein2GeneFromEnsembl`: New utility function that takes Ensembl protein
  identifiers as input, and returns corresponding gene identifiers and gene
  names (i.e. HUGO gene symbols).

### Minor changes

- Reworked some internal code in `makeGRangesFromEnesmbl` to enable export of
  new `getEnsDb` function.<commit_msg>Bump minor version, due to BiocFileCache change<commit_after>## basejump 0.13.0 (2020-10-02)

### Major changes

- `Ensembl2Entrez`: Improved internal matching engine, to allow reverse matching
  of Entrez identifiers to Ensembl identifiers.
- Now exporting `Entrez2Ensembl`, which works like `Entrez2Ensembl`.
- New S4 class `Entrez2Ensembl`, which inherits `Ensembl2Entrez` structure.

### Minor changes

- `makeSummarizedExperiment`: No longer requiring primary `assay` defined to
  be named "counts". This isn't appropriate for `SummarizedExperiment` objects
  defined in the new DepMapAnalysis package.
- `makeGRangesFromEnsembl`: Include `geneSynonyms` column for supported
  organisms, including *Homo sapiens*.

## basejump 0.12.16 (2020-09-29)

### Minor changes

- `makeProtein2GeneFromEnsembl`: Improved error message on match failure. Now
  returns the protein IDs that failed to match more clearly.

## basejump 0.12.15 (2020-09-25)

### New classes

- `Protein2Gene`: `DataFrame` with `proteinID`, `geneID`, and `geneName`
  columns. Use corresponding `makeProtein2GeneFromEnsembl` to generate object
  simplify using Ensembl protein IDs as input.

### New functions

- `getEnsDb`: Now exporting function that was used internally to obtain `EnsDb`
  object from AnnotationHub.
- `makeProtein2GeneFromEnsembl`: New utility function that takes Ensembl protein
  identifiers as input, and returns corresponding gene identifiers and gene
  names (i.e. HUGO gene symbols).

### Minor changes

- Reworked some internal code in `makeGRangesFromEnesmbl` to enable export of
  new `getEnsDb` function.
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