## basejump 0.12.4 (2020-03-15)

### Minor changes

- `matchEnsemblReleaseToURL`, `matchHumanOrthologs`: update unit tests to
  reflect Ensembl server migration, which has rendered Ensembl archives
  inaccessible via biomaRt until March 24th. Unit tests now check against
  current release instead of a pinned archive release.

## basejump 0.12.3 (2020-02-24)

### Minor changes

- `makeSingleCellExperiment`, `makeSummarizedExperiment`: Removed `spikeNames`
  support due to a breaking change in SingleCellExperiment, which has removed
  `isSpike` in favor of `altExps`. Refer to the SingleCellExperiment
  documentation for updated current best practice for handling spike-in
  transcripts, which now requires slotting a separate SummarizedExperiment
  object containing things like ERCCs inside the main SingleCellExperiment.

## basejump 0.12.2 (2020-02-18)

### Minor changes

- Migrating `pseudobulk` methods to pointillism package. Rethinking the approach
  used here to work better with per-cluster aggregation operations. Will be
  updated in the next pointillism release.

## basejump 0.12.1 (2020-01-30)

### Major changes

- Reworked `aggregate`, `aggregateCols`, `aggregateRows` support to reflect
  internal migration away from Matrix.utils dependency.

### Minor changes

- NAMESPACE fix for unexpected removal of Matrix.utils from CRAN. Now defining
  the previously imported aggregate.Matrix function directly here in basejump.
- `aggregate`: Now defining matrix method.
- `aggregate*` generics now consistently use "x" instead of "object".

## basejump 0.12.0 (2020-01-20)

### Major changes

- Migrated functions from brio (now renamed to pipette), freerange, and
  transformer, in preparation for Bioconductor submission and reviews.
- Updated messages to utilize the cli package.

## basejump 0.11.24 (2020-01-08)

### New functions

- `integerCounts`: Simple method support for returning a rounded integer counts
  matrix. Intended primarily for downstream handoff to bulk RNA-seq differential
  expression callers, such as DESeq2.

### Minor changes

- Updated dependency package version requirements. Needed primarily for bug
  fix in transformer, improving `mutateAll` functionality.

## basejump 0.11.23 (2019-11-19)

### Minor changes

- Updated package documentation to support roxygen2 7.0 update.
- Reworked `formalsList` global slightly. Using the `synesthesia` color palette
  for `heatmap.color` argument doesn't always perform well enough, so I'm
  switching to a blue/black/yellow palette defined by `blueYellow` in acidplots
  instead for `heatmap.color`. The `synesthesia` palette performs really well
  for correlation heatmaps, and is now recommended by default via the
  `acid.heatmap.correlation.color` global now instead.
- `filterCells`: Improved internal sampleName / sampleID handling.

## basejump 0.11.22 (2019-11-11)

### New functions

- `correlation`: Added S4 method support that mimics base `cor` methods, but
  is more flexible, supporting additional arguments via `...` in generic. This
  way we can provide intelligent and quick correlation calculations for nested
  assays inside a `SummarizedExperiment` and for `DESeqResults`
  (see DESeqAnalysis package).

## basejump 0.11.21 (2019-11-07)

### Major changes

- Updated Bioconductor dependencies to require new 3.10 release.

### Bug fixes

- `filterCells` requires an internal `decode` step to handle `Rle` evaluation,
  which worked previously in Bioconductor 3.9 release.
- Updated unit tests to reflect `SingleCellExperiment` example object resave
  in acidtest 0.2.7 update, which changed the numbers.

## basejump 0.11.20 (2019-10-24)

### New reexports

- Reexporting `metadata2` and `metadata2<-` functions from transformer.
  These will be used internally in the pending DESeqAnalysis update.

## basejump 0.11.19 (2019-10-23)

### New functions

- Genome version detection: `ensemblVersion`, `gencodeVersion`, `refseqVersion`,
  `flybaseVersion`, `wormbaseVersion`. Similar shell variants are available in
  the [koopa][] package.

### Minor changes

- Moved some low-level functions to new [acidbase][] package. Updated NAMESPACE
  and reexports to reflect these changes.

## basejump 0.11.18 (2019-10-13)

### Minor changes

- `importSampleData`: Pipeline now defaulting to "none" instead of "bcbio",
  since this flag is now properly hard coded in bcbio R packages.
  Added new Constellation (CPI) pipeline option.
- `makeSampleData`: Now checks for all NA columns and rows, similar to approach
  in `importSampleData`. This helps improve return consistency. Automatic
  rowname setting has been tweaked a bit to no longer attempt to remove original
  ID column.

## basejump 0.11.17 (2019-10-09)

### Minor changes

- `makeSampleData`: Made function slightly more flexible. Now allowing automatic
  rowname coercion from columns ("sampleID", "rowname", "rn"), similar to
  approach employed by data.table and tibble packages.
- Now exporting `stripGeneVersions` alias, which uses the same code internally
  as `stripTranscriptVersions`.

### Disabled methods

- Disabled DelayedArray class methods for `calculateMetrics`,
  `estimateSizeFactors`, and `nonzeroRowsAndCols` until `is_pristine` bug in
  DelayedArray v0.11.8 is fixed on Bioconductor Devel (3.10). This is causing
  unit tests to fail otherwise.
  See [related issue](https://github.com/Bioconductor/DelayedArray/issues/55)

## basejump 0.11.16 (2019-09-25)

### Minor changes

- Migrated S4 methods from syntactic that work on Bioconductor classes here.
  This keeps the syntactic package very light weight and focused only on
  character string sanitization.

## basejump 0.11.15 (2019-09-16)

### Major changes

- `melt`: Updated `min` and `minMethod` defaults for `matrix` method. The `min`
  argument now defaults to `-Inf`, and the `minMethod` now defaults to
  `"absolute"`, instead of `"perRow"`, since this behavior is more intuitive to
  the user.

### Minor changes

- `nonzeroRowsAndCols`: Added `assay` argument, switching from internal `counts`
  usage, to make the `SummarizedExperiment` method more flexible.

## basejump 0.11.14 (2019-09-09)

### Minor changes

- `mcolnames`: Moved S4 methods previously defined in syntactic here.
- Improved website documentation.

## basejump 0.11.13 (2019-09-06)

### Major changes

- `autopadZeros`: Added improved support for detection and automatic handling
  of zeros in need of padding on the left side of a character vector. This
  addition is necessary for handling of Genewiz processed FASTQ file names.
- `makeTx2Gene` functions now support `ignoreTxVersion` argument, similar to
  conventions defined in tximport package.

### Minor changes

- `importSampleData`: Updated to tentatively support a general pipeline via the
  "none" argument. In this case, only a `sampleID` column is required in
  metadata. This is been developed in conjunction with my new Genewiz to
  kallisto Nextflow processing pipeline being implemented at CPI.
  

## basejump 0.11.12 (2019-09-03)

### Minor changes

- `melt`: Added method support for contingency `table` class.
- Removed `set_*` reexports from magrittr packages.

## basejump 0.11.11 (2019-08-27)

Updated R dependency to 3.6.

### New functions

- `melt`: Added S4 methods for melting data into long format. Provides support
  for `matrix`, `Matrix`, `DataFrame`, `SummarizedExperiment`, and
  `SingleCellExperiment` currently.
- `nonzeroRowsAndCols`: Quickly remove non-zero rows and columns from a matrix
  or `SummarizedExperiment`.

### Major changes

- Migrated `EggNOG` and `PANTHER` S4 classes to separate packages.

### Minor changes

- `calculateMetrics`: Now calls `nonzeroRowsAndCols` internally first when
  `prefilter = FALSE`, speeding up calculations significantly for very large
  `SingleCellExperiment` objects. This was added to improve loading of example
  unfiltered 10X Genomics Chromium data.

### Deprecations

- Deprecated `readSampleData` and `readTx2Gene` in favor of `importSampleData`
  and `importTx2Gene`, respectively.

## basejump 0.11.10 (2019-08-22)

### Minor changes

- `makeSummarizedExperiment`: Now automatically handles non-Ensembl gene symbols
  present in assays that aren't defined in `rowRanges`. This applies primarily
  to 10X Cell Ranger v3 output, which includes some non-Ensembl gene symbols:
  CD11b, CD4, CD8a, HLA-DR, IgG1, PD-1, etc. The function still intentionally
  errors on unannotated Ensembl features, which often indicates an accidental
  release version mismatch.
- Updated dependency versions.

## basejump 0.11.9 (2019-08-21)

### Minor changes

- `meltCounts`: Added initial method support for `SingleCellExperiment`.
  Currently requires deparsing of the count matrix to call `reshape2::melt`.
  Returns columns with S4 run-length encoding (Rle) applied.
- `mapGenes`: Converted warning to message when `strict = FALSE`.

## basejump 0.11.8 (2019-08-19)

### New functions

- Migrated `readSampleData` and `readTx2Gene` from bcbioBase.
- Reworked `readSampleData` internal code, but still supporting bcbio pipeline
  conventions (i.e. "description" column for samples) as the default. I've
  reworked this approach so we can also call `readSampleData` inside the
  Chromium package (for 10X Genomics single-cell RNA-seq data) without having
  to depend on the bcbio R packages.
- Reexporting new dplyr-like methods that support S4 `DataFrame`:
  `inner_join`, `left_join`, `right_join`, `full_join`, `anti_join`;
  `mutate_all`, `mutate_at`, `mutate_if`;
  `select_all`, `select_at`, `select_if`.

### Major changes

- Removed dplyr and magrittr dependencies in internal code, where applicable.
- `aggregateCols`: Sped up return by calling `SingleCellExperiment` rather than
  `makeSingleCellExperiment`. Note that this now doesn't return session
  information in the object.
- `cell2sample`: Renamed return from `tibble` to `tbl_df`, for consistency.
- Made some previous deprecated functions still used in bcbioRNASeq v0.2 release
  series (which has now been updated to v0.3) defunct. This applies primarily
  to `assert*` functions that have been reworked using a goalie approach.
- `estimateSizeFactors`: Removed option to calculate "deseq2-median-ratio"
  using DESeq2. We may revisit this idea in a future release.
- `makeSampleData`: Improved internal code for `DataFrame` method.

### Minor changes

- Updated basejump dependencies, in preparation for bioconda release update
  supporting bcbioRNASeq.
- Now importing AnnotationDbi, BiocParallel, Biostrings, and biomaRt.
- Safe to import `select` from AnnotationDbi, now that we're no longer depending
  on dplyr.
- Switched to using `droplevels` instead of `relevel` on S4 objects internally,
  where applicable. This is better supported by S4Vectors package.
- Simplified reexport documentation for S4 functions and methods.

## basejump 0.11.7 (2019-08-13)

### Minor changes

- `filterCells`: Improved downstream handling of `nCells` argument.
  Ensure double filtering is still allowed.

## basejump 0.11.6 (2019-08-12)

### Minor changes

- Updated goalie dependency.
- Tightened up `appendToBody` and `methodFormals` calls to have better backward
  compatibility with R 3.5.
- `calculateMetrics`: Bug fix for getting `rowData` via `mcols` without
  `use.names = TRUE`. This improves Bioconductor backward compatibility.
  Also updated internal code to call `hasMetrics` from goalie.
- Made `separatorBar` defunct. Use `separator` function instead.

## basejump 0.11.5 (2019-08-11)

### New functions

- `calculateMetrics`: Migrated code here from bcbioSingleCell. Improved method
  to support `DelayedArray` class for large matrices.

### Minor changes

- Improved code coverage and adjusted unit tests for breaking changes seen due
  to new covr update.

## basejump 0.11.4 (2019-08-07)

### Major changes

- `makeSampleData`: Switched to S4 method that works on `data.frame` and
  `DataFrame` class objects. Enforcing lower camel case for column names.
- `makeSummarizedExperiment` and `makeSingleCellExperiment`: Switched to S4
  method approach that currently requires `SimpleList` input for assays.
  Previously, we allowed `list` input for assays, but we're tightening this up
  to simply the package code base and improve consistency.
- `aggregate` methods now consistently return the primary assay named as
  `counts`. This follows the recommended conventions defined in
  SingleCellExperiment. Aggregation functions will now intentionally fail for
  `SummarizedExperiment` objects that don't contain an assay named `counts`.

### Minor changes

- Improved documentation consistency by offloading `params.Rd` file to new
  acidroxygen package. This will be linked in the other Acid Genomics packages.
- Updated unit tests to follow new package conventions (see above changes).

## basejump 0.11.3 (2019-07-30)

100th release!

### Minor changes

- `mapCellsToSamples`: Relaxed grep matching on `cells` input to support legacy
  bcbioSingleCell objects. This change was needed to improve `updateObject`
  method in the upcoming bcbioSingleCell update.

## basejump 0.11.2 (2019-07-29)

### Minor changes

- Reexporting new functions in syntactic: `makeLabel`, `makeTitle`, `makeWords`.
- Updated documentation to include modification timestamp.

## basejump 0.11.1 (2019-07-24)

### Minor changes

- Added back deprecated assert checks that are required for bcbioRNASeq v0.2
  release series.

## basejump 0.11.0 (2019-07-22)

Start of new release series. Version bump reflects changes in dependency
packages. See the acidtest, bioverbs, freerange, syntactic, and transformer
release notes for more details.

## basejump 0.10.12 (2019-07-18)

### Minor changes

- Bug fix for `combine` method on SummarizedExperiment. Needed to ensure row
  names are assigned on rowData to provide backward compatibility for Bioc 3.7.
- Improved unit test exceptions on Docker and AppVeyor.
- Improved installation instructions.
- `mapGenesToRownames`: Improved matching for `SummarizedExperiment` objects
  that don't contain gene-to-symbol mappings defined in `rowData`.
- `meltCounts`: Improved factor handling. Also added `matrix` method support.
  Added advanced option to disable `minCounts` filtering, by setting as `NULL`.

### Deprecations

- Tightened up the list of deprecated functions.

## basejump 0.10.11 (2019-07-17)

### Minor changes

- Made `theme_midnight` and `theme_paperwhite` defunct, in favor if variants in
  new [acidplots][] package.
- Decreased the number of functions reexported from goalie package.
- Updated basejump dependency package versions.
- Improved Travis CI Docker configuration.

## basejump 0.10.10 (2019-06-08)

### New functions

- `matchEnsemblReleaseToURL`: Takes an Ensembl release version (e.g. `96`) as
  input and returns the corresponding archive URL.
- `matchHumanOrthologs`: Convenience function that wraps biomaRt package to
  map model system gene identifiers to HGNC IDs and symbols. This is
  particularly useful for running orthologus GSEA with our pfgsea package.

### Major changes

- `combine` method for `SummarizedExperiment` now includes all matrices defined
  in `assays` slot. Also improved support for `colData` handling on subsets
  where `NA` values have been removed.

### Minor changes

- `Gene2Symbol`: Modified `format` formal to use "unmodified" instead of "long",
  which is more intuitive.
- `makeGene2Symbol`: Added support for `format` argument, similar to
  `Gene2Symbol` generator function.

## basejump 0.10.9 (2019-05-29)

### Minor changes

- Relaxed the deprecations on some functions to provide backward compatibility
  support for bcbioBase and bcbioRNASeq packages: `readFileByExtension`,
  `readYAML`, `fixNA`.
- Now ensuring `theme_midnight` and `theme_paperwhite` are deprecated but
  exported with support, by suggesting acidplots package.
- Added back defunct function warnings: `assertHasRownames`, `tx2geneFromGFF`.

## basejump 0.10.8 (2019-05-05)

### Major changes

- Now pinned to R >= 3.5.

## basejump 0.10.7 (2019-04-30)

### New functions

- Added method support for `alphaThreshold` and `lfcThreshold` against
  `Annotated` class. These values get stored in the `metadata` slot of the
  object.

## basejump 0.10.6 (2019-04-29)

### New functions

- `showHeader`: Utility function for `show` methods defined in other packages.

### Minor changes

- Updated basejump dependencies (see `DESCRIPTION` for details).

## basejump 0.10.5 (2019-04-25)

### Minor changes

- Reworked S4 generic reexport method, in an attempt to get pkgdown to build
  vignette correctly. Otherwise, `sampleData` is erroring.

## basejump 0.10.4 (2019-04-22)

### Major changes

- `meltCounts`: Switched from using `nonzeroGenes` formal approach to
  `minCounts` and `minCountsMethod`, which is more flexible.

### Minor changes

- Consolidated minimalism and firestarter code into acidplots package.
- Improve global options defined in `formalsList`.
- Added back basejump vignette.

## basejump 0.10.3 (2019-04-07)

### Minor changes

- Bug fix release for [freerange][] update. `emptyRanges` format has been
  renamed from `mcolsNames` to `mcolnames`.

## basejump 0.10.2 (2019-04-07)

### Major changes

- `aggregateRows`, `aggregateCols`, `aggregateCellsToSamples`: Improved internal
  code for SummarizedExperiment metadata handling. Applies primarily to colData
  and rowData juggling for these methods.
- `interestingGroups`: Reworked to define method against `Annotated` class.
  `SummarizedExperiment` inherits from this class, supporting `metadata`.
- `mapCellsToSamples`: Tightened up match assert checks.
- `mcolnames` now uses S4 methods, primarily against `Vector` class.
- `organism`: Reworked S4 methods. Added support for `Annotated` and
  `DataTable` classes from [S4Vectors][].

### Minor changes

- Added additional unit tests, to improve code coverage.
- Now covering the aggregation functions in better detail, using a minimal
  SingleCellExperiment object that works with `aggregateCols`.
- Consistently use "acid" prefix instead of "basejump" for global options.
- Miscellaneous working example improvements.
- `detectLanes`: Renamed primary argument from `object` to `path`. Improved
  `pattern` formal to evaluate `lanePattern` global.
- For S4 generators, renamed test paramter from `basejump.test` to `acid.test`.
- `sampleData`: Improved error message when `sampleName` factor column is
  missing.
- `zeroVsDepth` now returns `depth` column as `integer` instead of `numeric`.

## basejump 0.10.1 (2019-04-01)

### New functions

- `rankedMatrix`: New utility function for quickly performing ranked matrix
  calculations. Particularly useful for differential expression comparison
  across studies using log2 fold change or Wald test statistic.

### Minor changes

- Simplified reexport methods for functions that define S4 methods.

## basejump 0.10.0 (2019-03-28)

### Major changes

- Split out Ensembl (AnnotationHub/ensembldb) annotation processing and GFF/GTF
  file loading utilites to new [freerange][] package. All of these functions
  remain re-exported here in [basejump][]. This includes: `annotable`,
  `convertUCSCBuildToEnsembl`, `detectOrganism`, `emptyRanges`,
  `makeGRangesFromEnsDb`, `makeGRangesFromEnsembl`, `makeGRangesFromGFF`,
  `makeGRangesFromGTF`.
- Split out heatmap functions to firestarter package. This includes
  `plotHeatmap`, `plotCorrelationHeatmap`, and `plotQuantileHeatmap`.
- Split out all ggplot2 functions to new minimalism package.

### Minor changes

- Offloaded `removeNA` and `sanitizeNA` code to [brio][] package, so these
  functions can be imported in thew new [freerange][] package.
- Moved `organism_mappings` internal dataset to [freerange][] package.

## basejump 0.9.16 (2019-03-23)

### Minor changes

- `convertSampleIDsToNames`: Removed code to assign `sampleName` column to
  `NULL`. This step doesn't work consistently for `DataFrame` across
  Bioconductor installations, and has been found to error on R 3.4 and the
  current bioc-devel on AppVeyor.
- Miscellaneous documentation fixes, removing extra formatting in titles.
- `makeGRangesFromGFF`: Compressed Ensembl GTF file example was erroring out
  on AppVeyor CI, due to Windows' poor handling of temp files on non-admin
  accounts. Switched to a non-gzipped example file to avoid this issue. Also
  removed tabular table from documentation, which currently doesn't render
  correctly via pkgdown.

## basejump 0.9.15 (2019-03-22)

### Minor changes

- Migrated code to [Acid Genomics][].

## basejump 0.9.14 (2019-03-18)

### Minor changes

- Additional bug fixes for `sampleData` and blacklisted metadata handling.

## basejump 0.9.13 (2019-03-18)

### Minor changes

- Updated dependencies, specificially brio and goalie.
- Miscellaneous documentation improvements.

## basejump 0.9.12 (2019-03-11)

### Major changes

- `makeGRangesFromGFF`: Reworked internal code, making it more modular. Added
  initial support for RefSeq GFF3 files. Also improved sanitization and special
  handling of files from FlyBase and WormBase.

### Minor changes

- `plotHeatmap` family: Bug fix needed for internal `is.na` call on
  `annotationCol`, which should be wrapped with `any` to return boolean. This
  errors (as it should) on R 3.6, but I missed it on R 3.5.
- Consolidating GRanges return code defined in `.makeGRanges`, which is run
  for both GFF file and ensembldb import. We've improved the Rle encoding steps
  here to work with complex GFF3 files (e.g. GENCODE).

## basejump 0.9.11 (2019-02-25)

### Minor changes

- Updated [transformer][] package reexports to include new [data.table][]
  coercion methods.
- Added additional useful compression function reexports from [brio][] package.

## basejump 0.9.10 (2019-02-17)

### Minor changes

- Working on making the current basejump code base completely backward
  compatible with bcbioBase v0.4.1 and bcbioRNASeq v0.2.8 release series.
- Now reexporting `goalie::bapply` and additional useful pipes from [magrittr][]
  package.
- Keeping the now deprecated `plotGene` generic reexported, while encouring
  users to update their code to use `plotCounts` instead.
- `interestingGroups`: Simplified internal assert checks, removing
  `matchesInterestingGroups`, which can become circular.

## basejump 0.9.9 (2019-02-11)

### Minor changes

- Code fixes to provide backward compatibility support for R 3.4. Tested using
  R 3.4.1 with Bioconductor 3.6 release.
- Needed to add `unname` to some assert checks for expected `logical(1)` return,
  which only happens in R 3.4 but not R 3.5.
- `uniteInterestingGroups`: Improved internal assert checks and name handling.

## basejump 0.9.8 (2019-02-08)

### Minor changes

- Deprecating `plotGene` in favor of `plotCounts`. This change will be reflected
  in future updates of packages that depend on [basejump][], including the bcbio
  R packages.
- Split out subpackage reexports into separate files.
- Reexporting `assert` from goalie package.

## basejump 0.9.7 (2019-01-23)

### Minor changes

- `decode` and `encode` are properly reexported from [brio][].
- Updated Travis CI and AppVeyor CI configurations.

## basejump 0.9.6 (2019-01-22)

### Minor changes

- Note that S4Transformer package import has been renamed to transformer.
- Needed to add `decode` call internally for some plotting functions, to ensure
  that run-length encoded (Rle) rowData gets handled correctly.
- Bug fix for internal `interestingGroups` handling in plot functions.

### Offloaded to brio

- `decode`, `encode`. These are useful for data sanitization. Still re-exported
  here in [basejump][].

### Offloaded to goalie

- `printString`. This is a low-level function that is useful for setting the
  cause attribute in error messages. Still reexported here in basejump.

### Deprecations

- `sanitizeRowData` has been deprecated in favor of `atomize`.
- `sanitizeAnnotable` deprecation has been updated to point to `atomize`.

## basejump 0.9.5 (2019-01-22)

### Minor changes

- Updated basejump subpackage dependencies.
- Needed to add `decode` call internally for some plotting functions, to ensure
  that run-length encoded (Rle) rowData gets handled correctly.
- Bug fix for internal `interestingGroups` handling in plot functions.

### Offloaded to brio

- `decode`, `encode`. These are useful for data sanitization. Still re-exported
  here in [basejump][].

### Offloaded to goalie

- `printString`. This is a low-level function that is useful for setting the
  cause attribute in error messages. Still reexported here in basejump.

### Deprecations

- `sanitizeRowData` has been deprecated in favor of `atomize`.
- `sanitizeAnnotable` deprecation has been updated to point to `atomize`.

## basejump 0.9.4 (2019-01-12)

### Minor changes

- Consolidated reexports from [basejump][] sub-packages into `reexports.R` file.
- Miscellaneous documentation updates, improving link appearance for functions
  exported in other packages.

## basejump 0.9.3 (2019-01-08)

### Minor changes

- Reorganized imports in `DESCRIPTION` file to make them more human readable.
  Note that [basejump][] sub-packages are imported first, then [Bioconductor][]
  packages, followed by [CRAN][] packages, and required default packages.
- Split out NAMESPACE imports into a separate `imports.R` file.

## basejump 0.9.2 (2019-01-07)

This release defines the initial point where [basejump][] becomes even more
modular, offloading some functions to new [brio][], [syntactic][], and
S4Transformer packages.

Note that all offloaded functions will continue to be reexported in
[basejump][]. If you notice a function that is missing and not correctly
re-exported, please file an issue.

Note that S4Transformer has since been renamed to [transformer][].

### Offloaded to S4Transformer

- `as` coercion methods moved to S4Transformer package. This methods define our
  useful interconversions between Bioconductor and tidyverse data classes,
  including `DataFrame` and `tbl_df` (tibble).
- `coerceS4ToList` / `flatFiles`.

### Offloaded to bb8

- `cleanSystemLibrary`. This doesn't scale well to all installations and is
  really only intended for personal use, so bb8 package is more appropriate.
- Documentation functions, including `parseRd`, `RdTags`, `saveRdExamples`, and
  `tabular` are outside the scope of [basejump][].

### Offloaded to brio

- `basenameSansExt`.
- `dots`.
- `export`.
- `import`.
- `initDir`.
- `loadData`.
- `localOrRemoteFile`.
- `pasteURL`.
- `realpath`.
- `sanitizeColData`.
- `sanitizeRowData`.
- `sanitizeSampleData`.
- `saveData`.
- `transmit`.
- `writeCounts`.

### Offloaded to goalie

- `matchArgsToDoCall`.
- `MethodDefinition`.
- `standardizeCall`.

### Minor changes

- Added `nullOK` support to [goalie][] assert checks, where applicable.

## basejump 0.9.1 (2018-12-22)

This release defines the initial point where [basejump][] begins to import
[bioverbs][].

### Major changes

- Now importing generics using our [bioverbs][] S4 generic package. All generics
  previously defined in [basejump][] will continue to be reexported, to maintain
  backward compatibility for reverse dependencies (revdeps).

### Minor changes

- `aggregateCellsToSamples`: Split out S4 method to a separate file. Previously
  was defined in `aggregate-methods.R`.
- Reorganized collapse family of functions. Refer to changes in
  `collapse-methods.R`, which is now split out to `collaseToString-methods.R`.
- Split out the markdown family of functions back out into separate files.
- `matchesGene2Symbol`, `matchesInterestingGroups`: Reworked internal code and
  moved to separate files. No longer relies upon `makeTestFunction` from
  [checkmate][] package.

### Documentation

- Switched documentation titles to sentence case from title case. It's generally
  more readable.

## basejump 0.9.0 (2018-12-12)

I bumped the release series from v0.8 to v0.9 because this represents a
significant change to the internal codebase, where I have now switched to using
my new [goalie][] assert check engine from [assertive][].

### New functions

- `decode`: Decode S4 run-length encoding (Rle).
- `encode`: Apply S4 run-length encoding (Rle).
- `geneNames`: Convenience function that returns gene names (symbols) mapped to
  the stable, but not human-friendly gene identifiers.
- `matchesGene2Symbol`, `matchesInterestingGroups`: New functions designed to
  match corresponding `Gene2Symbol` objects or `interestingGroups`.
- `pasteURL`: Convenience function that generates URL strings.
- `sanitizeColData`: rework of previous `sanitizeSampleData` approach.

### Major changes

- Now using [goalie][] package instead of [assertive][] for internal assert
  checks. The new `goalie::assert` function is more flexible in many cases.
  Similarly, `goalie::validate` is now being used in place of
  `assertthat::validate_that`.
- `plotHeatmap` now calculates the z-score normalization internally, rather than
  relying upon the codebase inside [pheatmap][].
- `export`: Improved `SummarizedExperiment` method to also write `Gene2Symbol`
  and `Ensembl2Entrez` mappings to disk, when defined. The human-friendly output
  formal has been renamed from `human` to `humanize`, to reflect an action
  (verb). This corresponds better to our `humanize` generic function. Also
  reworked some internal code that handles output of colData and rowData to
  disk.
- `makeGRangesFromEnsembl`: Switched to using S4 run-length encoding (Rle) in
  our metadata column (mcols) return. This functionality matches the conventions
  used by GenomicRanges in the `GRanges` return, and reduces the memory
  footprint of very large annotation objects.

### Minor changes

- Note that some internal instances of `has_length` aren't quite strict enough.
  Switch to using `length(x) > 0L` or improved `hasLength` assert check defined
  in the [goalie][] package.
- `geneSynonyms`: Switched to using new `pasteURL` function internally instead
  of using `paste` with `/` separator.
- `HGNC2Ensembl` generator: switch to using `pasteURL` internally.
- `loadData`, and other related load family functions: simplified internal code
  using our new [goalie][] asserts.

### Deprecations

- Removed `assertFormalGene2symbol` from deprecations.

### Documentation

- Improved documentation style throughout the package, switching from the usage
  of scalar types like `string` to `character(1)`, and `boolean` to
  `logical(1)`. This better matches the actual data structure in R. Some other
  packages like [checkmate][] also use this convention, which I think is more
  readable than my previous approach.

## basejump 0.8.8 (2018-12-03)

### New functions

- `deg`: Utility function to quickly obtain differentially expressed gene
  (DEG) identifiers as a character vector.

### Major changes

- `plotHeatmap`: Now defining row scaling internally, rather than relying on the
  functionality defined in `pheatmap`.

## basejump 0.8.7 (2018-12-01)

### New functions

- `humanize`. New generic that enables easy conversion to human-friendly column
  and/or row names. Useful for CSV file export in particular.

### Minor changes

- `export`: Added `humanize` argument support.
- Improved grep pattern matching inside `makeNames` functions
  (e.g. `.sanitizeAcronyms`).
- `sampleData`: Improved blacklist pattern matching against `Seurat` objects
  for `SingleCellExperiment` method.

## basejump 0.8.6 (2018-11-30)

### Minor changes

- Now importing `hasUniqueCols` from goalie. Switched from previous approach
  using `areSamplesUnique`.
- Documentation improvement for `genomeBuild`, used in `makeGRanges` functions.
- Miscellaneous documentation improvements to pass build checks.

## basejump 0.8.5 (2018-11-29)

### New functions

- `relevelRowRanges`, `relevelColData`.

### Deprecations

- `markdownPlotlist`. Renamed to `markdownPlots`.

### Minor changes

- `autopadZeros`: Improved internal code to keep track of names for `character`
  method. Also added method support for `SummarizedExperiment`, which works on
  the column names (e.g. sample names) only by default.
- `Ensembl2Entrez`: Simplify validity check to require `integer` in `entrezID`
  column. Also reworked and improved internal code that supports run-length
  encoding (Rle) using `decode`.
- `export`: Improved documentation for `name` argument.
- `makeGRangesFromEnsembl`: Improved messages to user.
- `plotCountsPerBiotype`: Improved error messages for when the biotype isn't
  defined.
- `plotPCA`: Add support for unique sample detection with `areSamplesUnique`,
  similar to the approach used in the bcbioRNASeq quality control R Markdown.
- `sampleNames`: Simplified `sampleName` extraction, using `[[` internally.
- Miscellaneous documentation fixes.
- Updated unit test for `sanitizeRowData`.

## basejump 0.8.4 (2018-11-28)

### New functions

- `autopadZeros`. Useful for padding zeros inside of a character vector.
- `basenameSansExt`. Quickly get the basename without the file extension for
  desired file path(s). Surprisingly, this isn't defined in the tools package
  so I wrote my own.
- `cleanSystemLibrary`. I ran into some shared library configuration issues
  on the Azure infrastructure, so this utility function is useful for checking
  wheter an R installation has a clean library.
- `plotGenderMarkers`: Migrated the `SummarizedExperiment` method from
  bcbioRNASeq package.

### Minor changes

- Split out call functions defined in `calls.R` into separate R files.
  Refer to `dots`, for example.
- Split out `environment.R` into separate R files. See `detectHPC` for example.
- Miscellaneous documentation improvements.

## basejump 0.8.3 (2018-11-25)

### Minor changes

- Improved usage of `assertthat::validate_that` in S4 class validity checks.
  Removed former approach using internal `.valid` function.
- Temporarily soft deprecated some functions that will be formally deprecated
  in a future release. See `deprecated.R` file.
- `interestingGroups` doesn't attempt validity check using `validObject` by
  default, which can be enabled instead using `check = TRUE`.
- `sampleData`: Tightened up internal assert checks.
- `PANTHER`: Minor tweaks to internal variable names inside `.splitTerms`.
- `transmit`: Improved messages. Temporarily disabled working example, since it
  consistently fails on [Travis CI][].

## basejump 0.8.2 (2018-11-19)

### Major changes

Migrating some additional base code that can be dispatched on either
`SummarizedExperiment` or `SingleCellExperiment` from the bcbio R packages.
We're going to split out some of the single-cell RNA-seq functionality into
separate packages, since a lot of my work moving forward deals with the 10X
Genomics Cell Ranger platform, rather than the bcbio-supported inDrops platform.

In particular:

- `barcodeRanksPerSample`.
- `filterCells`.
- `plotBarcodeRanks`.
- `plotCellCounts`.
- `plotGenesPerCell`.
- `plotMitoRatio`.
- `plotMitoVsCoding`.
- `plotNovelty`.
- `plotReadsPerCell`.
- `plotUMIsPerCell`.
- `plotUMIsVsGenes`.

### Minor changes

- Migrated some `plotHeatmap` and `plotPCA` code from bcbio R packages.
- Added new `formalsList` global variable, which stashes `getOption` defaults
  used in some functions, namely the save/load functions and some plotting
  functions.
- Switched to using `formalsList` along with `formals` declaration internally
  to make the parameters more consistent across functions.
- Miscellaneous fixes to working examples and documentation.
- Split out sanitization functions into separate R files (e.g. `removeNA`).

## basejump 0.8.1 (2018-11-15)

### Major changes

The split-out sub-package approach isn't working quite right, so the code base
has been consolidated back into a single basejump package. Development toward
splitting the package will continue, but a conceptual re-imagining of how to
organize the functions is needed.

## basejump 0.8.0 (2018-11-11)

### Major changes

This release is the beginning of an attempt to rework the basejump codebase a
bit and make the package easier to unit test on [Travis CI][]. bcbio R packages
will be pinned to v0.7.2 during this development period.

Here we are working to split out the functionality of basejump into
several, smaller sub-packages:

- basejump.annotations
- basejump.assertions
- basejump.classes
- basejump.coercion
- basejump.developer
- basejump.experiment
- basejump.generics
- basejump.globals
- basejump.io
- basejump.markdown
- basejump.plots
- basejump.sanitization

## basejump 0.7.2 (2018-08-29)

### New functions

- `assertAllAreURL`.
- `assertAllAreValidNames`.
- `validNames`.

### Major changes

- Added a draft vignette explaining the functions available in the package.
- `gene2symbol`, `makeGene2symbolFromEnsembl`, and
  `makeGene2symbolFromGFF` functions now support the `unique` argument, which
  returns sanitized values in the `geneName` column, ensuring there are no
  duplicates. This is enabled by default (recommended) but can be disabled using
  `unique = FALSE`. This functionality was added to ensure consistent gene name
  handling in single-cell RNA-seq analyses.
- `saveData` now supports `basejump.save.ext` and `basejump.save.compress`
  global options, so the desired file type (e.g. RDS instead of RDA) and
  compression (e.g. xz instead of gzip) can be easily specified for an entire
  project.

### Minor changes

- `sampleNames` now supports assignment for `SummarizedExperiment` method.
- Now exporting `lanePattern` regular expression pattern as a global, which was
  previously defined in the [bcbioBase][] package.
- Bug fix for `as` coercion method support. Need to ensure
  `exportMethods(coerce)` is included in `NAMESPACE` file, otherwise
  `tibble` coercion using `as(x, "tbl_df")` won't work when called from an
  Rscript without the package library loaded. Thanks @roryk for noticing this.
- Updated `gene2symbol` generic to use `...`, since we've added the
  `unique = TRUE` argument in this release.
- `annotable`: Moved to `makeGRanges.R` file, and improved the internal code
  to export supported formals also used in `makeGRangesFromEnsembl`. The
  function should work exactly the same as previous releases, but now with
  clearer supported arguments in the documentation.
- Skipping code coverage for `cleanSystemLibrary`, since [Travis CI][]
  installs packages into the system library, and causes this check to return
  `FALSE`.
- Consistently using `as(from, "tbl_df")` for internal tibble coercion in all
  functions.
- `geneSynonyms` and `panther`: `organism` argument matching no longer suggests
  a default.
  The current list of supported organisms is in the documentation, and described
  in the internal `match.arg` call.
- All `SummarizedExperiment` methods use `validObject` validity checks, where
  applicable.
- Consolidated documentation for all `makeGRanges`, `makeGene2symbol`, and
  `makeTx2gene` functions.
- Heatmap functions: simplified the internal code responsible for defining
  `annotationCol` and `annotationColors` automatically.
- `sampleData`: Made validity check stricter, requiring `sampleName` column
  to be defined, otherwise the function will intentionally error.
- Now using `formals` internall to keep ggplot2 theme formals consistent.
- Updated example data scripts and resaved internal data.
- Updated contribution guidelines in `CONTRIBUTING.md` file.

## basejump 0.7.1 (2018-08-18)

### New functions

- `cleanSystemLibrary`: Utility function to check whether a user has installed
  packages into the [R][] system library. Refer to `.libPaths` documentation
  for more information on library paths.

### Major changes

- Now using `build` instead of `genomeBuild` for [Ensembl][] annotation
  functions. The `genomeBuild` argument still works but now will inform the user
  about the change.

### Minor changes

- Migrated `prepareTemplate` from [bcbioBase][] package. Simplifed this
  function to copy all files inside `extdata/rmarkdown/shared` within a
  specified package. Currently in use for [bcbioRNASeq][], [bcbioSingleCell][],
  and the new [pointillism][] clustering package.
- Made [Ensembl][] release matching stricter, based on the metadata columns.

## basejump 0.7.0 (2018-08-07)

In this release, we are migrating some of the S4 generics previously exported
in the [bcbioBase][] package. We are consolidating these functions here for
simplicity and stability.

### New functions

- `makeSummarizedExperiment`: Renamed `prepareSummarizedExperiment`,
  previously exported in the [bcbioBase][] package. We are using the `make`
  prefix here for consistency (see other gene annotation functions).
- Migrated S4 generics and methods from [bcbioBase][]: `flatFiles`,
  `metrics`, `plotCorrleationHeatmap`, `plotGene`, `plotHeatmap`,
  `plotQC`, and `plotQuantileHeatmap`.

### Major changes

- Now using `curl::has_internet` internally to check for Internet connection.
  This applies to the annotation functions that query web databases.
- Added coercion method support for converting a `SummarizedExperiment` to
  an unstructured `list`. This is the method used internally for `flatFiles`.

## basejump 0.6.4 (2018-08-03)

### New functions

- `matchInterestingGroups`: New developer function to automatically handle
  `interestingGroups` argument used across various plotting functions and in the
  [bcbio][] infrastructure packges.

## basejump 0.6.3 (2018-08-01)

### Minor changes

- Migrated `separatorBar` and `updateMessage` global export from [bcbioBase][].
  Improved `separatorBar` appeareance to automatically scale to current session
  width, using `getOption("width")`.

## basejump 0.6.2 (2018-07-31)

### New functions

- `convertSymbolsToGenes`: provides `SummarizedExperiment` method support for
  converting objects containing gene symbols ("geneName") as rownames back to
  gene identifiers ("geneID").
- `eggnog`: quickly download current annotations from [EggNOG][] database.
  Useful for annotating gene-to-protein matches; currently in use with the
  [brightworm][] RNAi screening package, which contains [WormBase][] gene ID and
  [EggNOG][] ID annotations.

### Major changes

- Now suggesting [BiocManager][] instead of [BiocInstaller][] for installation.
- `broadClass` now supports `GRanges` and `SummarizedExperiment`. Support for
  `data.frame` and/or `DataFrame` class objects has been removed.

### Minor changes

- `convertGenesToSymbols` and `convertTranscriptsToGenes` now have
  `organism` and `gene2symbol` arguments set `NULL` by default.
- Upgraded to [roxygen2][] v6.1 for documentation, which improves handling of
  aliases in the Rd manual files.
- Added `dplyr::pull` to reexported functions.
- Improved package documentation by declaring the supported class(es) for
  each function argument.
- Moved `foldChangeToLogRatio` and `logRatioToFoldChange` constructors into
  `numeric` method declarations.
- Simplified internal code for `gene2symbol` `SummarizedExperiment` method.
- `toStringUnique` now uses `x` instead of `atomic` as primary argument.

## basejump 0.6.1 (2018-07-21)

### Minor changes

- Bug fix for `convertGenesToSymbols` method for `SummarizedExperiment`.
  Previously, if `geneName` column was a factor, this function would error.
  This issue has been fixed by ensuring that the symbols provided in `geneName`
  are coerced to a character vector.
- Improved [conda][] installation instructions.

## basejump 0.6.0 (2018-07-17)

### Major changes

- Now importing [SummarizedExperiment][] package and providing basic method
  support for generics that were previously used in the [bcbioBase][] package.
- Improved GFFv3 handling in `makeGRangesFromGFF` and other GFF utility
  functions, including `makeGene2symbolFromGFF` and `makeTx2geneFromGFF`.
  Note that `makeGRangesFromGFF` now returns additional metadata columns
  accessible with `S4Vectors::mcols`, and that these columns are now sorted
  alphabetically.

### Migrated functions

Previously, these functions were exported in the [bcbioBase][] package, but
they provide non-[bcbio][]-specific functionality, and should be included here
in the [basejump][] package instead:

- `assertFormalInterestingGroups`.
- `gene2symbol`.
- `interestingGroups`, `uniteInterestingGroups`.
- `sampleData`, `sanitizeSampleData`.
- `sampleNames`.
- `selectSamples`.

Providing basic `SummarizedExperiment` class method support for `counts`.

### Minor changes

- `geometricMean` generic was not exported correctly.

## basejump 0.5.11 (2018-07-09)

### Minor changes

- Now requiring [ggplot2][] v3.0 internally.
- `theme_midnight` and `theme_paperwhite` now extend
  `ggplot2::theme_linedraw`, improving the consistency between these themes.
- Example data is now consistenly formatted using snake case: `rnaseq_counts`
  and `single_cell_counts`, instead of the previous camel case conventions:
  `rnaseqCounts`, `singleCellCounts`.
- Camel variants of the ggplot themes are now deprecated.
- Updated internal gene synonyms data from [NIH][].

## basejump 0.5.10 (2018-06-28)

### Minor changes

- Removed `makeNames` argument from `readFileByExtension` function. Use the
  `makeNames` family of functions manually after data import instead. This
  helps avoid unwanted sanitization of data.
- Simplified assert checks for internal load function.
- Improved code coverage.
- [AppVeyor CI][] updates to work with [Bioconductor][] 3.8 devel.

## basejump 0.5.9 (2018-06-12)

### Minor changes

- Markdown function consistency improvements. Now all relevant [Markdown][]
  functions use `text` as the primary argument, instead of `object`.

## basejump 0.5.8 (2018-06-05)

### Minor changes

- `makeGRangesFromEnsembl` now supports remapping of [UCSC][] genome build to
  Ensembl. However, this isn't recommended, and will warn the user.
- `convertUCSCBuildToEnsembl` now returns `NULL` instead of erroring on
  genome build match failure.
- `stripTranscriptVersions` now matches "`.`", "`-`", and "`_`" version
  delimiters.
- Made unused `dynamicPlotlist` function defunct.
- Consider deprecating `assertIsCharacterOrNULL` and
  `assertIsDataFrameOrNULL` in a future release.

### Infrastructure changes

- Reenable [Travis CI][] blocklist, excluding develop branch from checks.
- Reorganized documentation of deprecated and defunct functions.

## basejump 0.5.7 (2018-05-24)

### Minor changes

- Tweaked gray color accents for `theme_midnight` and `theme_paperwhite`.

## basejump 0.5.6 (2018-05-19)

### Minor changes

- Fixed NAMESPACE issue with `GenomeInfoDb::seqnames`.
- Improved `readGFF` working example to reflect switch to `GRanges` return.
- Added [macOS][] bioc-release image to [Travis CI][] build checks.

## basejump 0.5.5 (2018-05-15)

### Major changes

- `readGFF` now uses `rtracklayer::import` internally to return GFF file
  as a `GRanges` object instead of a `data.frame`.

### Minor changes

- `assertIsGFF` and `parseGFFAttributes` functions are now defunct.
- Simplified internal GFF handling code for `makeGRangesFromGFF`,
  `makeGene2symbolFromGFF`, and `makeTx2geneFromGFF`.

## basejump 0.5.4 (2018-05-08)

- Migrated `sanitizeSampleData` to [bcbioBase][] package.
- Updated [Bioconductor][] install method for 3.7.

## basejump 0.5.3 (2018-04-30)

### Minor changes

- Improved internal S4 method code for `fixNA` and `removeNA`.
- Tweaked gray accent colors in `theme_midnight` and `theme_paperwhite`.
  Now using British spelling internally for ggplot code.
- Improved `strip.background` for `theme_paperwhite`, removing the black box
  around the labels when facet wrapping is enabled.

## basejump 0.5.2 (2018-04-26)

### Minor changes

- Improved documentation for assert check functions.
- Deprecated `geomean` in favor of `geometricMean`.
- Simplified internal code for `grepString`.
- Added message during `hgnc2gene` call.
- Miscellaneous documentation fixes.
- Moved internal constructors into the S4 method definitions, where applicable.
- Simplified default parameter definition for `panther(organism = "XXX")`.
- Improved code coverage, using `nocov` where appropriate.

## basejump 0.5.1 (2018-04-16)

### Minor changes

- `emptyRanges`: Now using `match.arg` internally to capture `seqname`
  argument.
- Removed legacy `.assignCamelArgs` and `.assignCamelFormals` internal
  functions.
- Improved internal handling of XLSX files in `localOrRemoteFile`.

## basejump 0.5.0 (2018-04-13)

### New functions

- `emptyRanges` enables easy creation of placeholder ranges for `GRanges`
  objects, where transgene and FASTA spike-ins are needed.
- `hgnc2gene` enables easy mapping of [HGNC][] to [Ensembl][] gene
  identifiers.
- `mgi2gene` enables easy mapping of [MGI][] to [Ensembl][] gene identifiers.
- `panther` function enables easy querying of the [PANTHER][] website.
  Human, mouse, nematode worm, and fruit fly are currently supported. The
  specific [PANTHER][] release (e.g. 13) can be declared using the `release`
  argument. Otherwise, the function will return the most recent annotations
  from the [PANTHER][] website.
- Added `isURL` check function.
- `readJSON` adds support for JSON files. Like the other read functions, it
  supports both local files and remote URLs.

### ggplot2 themes

- `theme_midnight` and `theme_paperwhite` provide minimal, high contrast
  [ggplot2][] themes with bold sans serif labels.

### Major changes

- `loadData` now supports `.rda`, `.rds`, and `.RData` files. The function
  will error by design if multiple data extensions are detected inside the
  directory specified with the `dir` argument.

### Minor changes

- Consolidated assert check function code.
- Moved assertive imports to `basejump-package.R` file.
- Consolidated globals inside package to `globals.R` file.
- Removed internal `.biocLite` function. Now using `requireNamespace`
  instead, without attempting to install automatically.
- Added internal support for safe loading RDS files.
- Switched back to using `message`, `warning`, and `stop` instead of
  the [rlang][] equivalents.
- Improved internal method declaration using `getMethod` where applicable.
- `multiassignAsEnvir` is now recommended in place of
  `multiassignAsNewEnvir`.
- `readFileByExtension` will now attempt to use the [rio][] package for
  file extensions that are not natively supported.
- `writeCounts` now uses `mapply` internally.
- Migrated `assertFormalAnnotationCol` to [bcbioBase][] package.

## basejump 0.4.0 (2018-03-22)

### Major changes

- Introducing new functions for the acquistion of gene and transcript
  annotations from [Ensembl][]: `ensembl`, `genes`, and `transcripts`.
  These functions allow the return of `GRanges`, `DataFrame`, and `data.frame`
  class objects from [AnnotationHub][] using [ensembldb][].
- Improved internal `broadClass` definition code to match against chromosome
  from [Ensembl][] if available.
- `loadDataAsName` now works with unquoted names, improving consistency
  with `loadData` (non-standard evaluation).

### Minor changes

- Added new `convertUCSCBuildToEnsembl` function, for easy remapping of
  [UCSC][] to [Ensembl][] genome build names (e.g. `hg38` to `GRCh38`).
- Migrated matrix methods for `plotCorrelationHeatmap` here from
  [bcbioRNASeq][], for improved consistency with other heatmap functions.
- Exporting `makeNames` variant of `base::make.names` that sanitizes
  using underscores rather than dots.
- Converted `readYAML` from a generic to standard function.
- Added support for [AppVeyor CI][] code testing on [Windows][].
- Made [Travis CI][] build checks stricter, adding support for `BiocCheck`.
- Added new assert checks: `assertAreGeneAnnotations`,
  `assertAreTranscriptAnnotations`, `isAnImplicitInteger`.
- Simplified working examples for assert checks to just show successes.

### Deprecations

- `annotable` function has been deprecated in favor of the new `ensembl`
  function.
- `checkAnnotable` deprecated in favor of `assertIsAnnotable`.
- `checkGene2symbol` deprecated in favor of `assertIsGene2symbol`.
- `checkTx2gene` deprecated in favor of `assertIsTx2gene`.
- `assertFormalColorFunction` deprecated in favor of
  `assertIsHexColorFunctionOrNULL`.
- `initializeDir` deprecated in favor of `initializeDirectory`.
- Defunct: `summarizeRows`, `wash`, `packageSE`, `prepareSE`,
  `metadataTable`, `comp`, `revcomp`, `symbol2gene`.

## basejump 0.3.1 (2018-02-19)

- Now exporting all assert checks in camel case instead of snake case, to
  match consistency in the rest of the package.
- Added `sanitizeColData` function.
- Added `assertAllAreNonExisting` function.
- Now exporting `midnightTheme` as a `theme_midnight` alias to match the
  syntax in the [ggplot2][] package.
- Added working examples and code coverage for all assert check functions.
- Simplified the internal collapse code for `annotable` to simply work on
  the [Entrez][] identifier column (`entrez`). If a manually passed in data
  frame still has duplicates, the function will now abort instead of attempting
  to use `collapseToString`.
- Added [ggplot2][] color palette assert checks:
  `assertColorScaleContinuousOrNULL`, `assertColorScaleDiscreteOrNULL`,
  `assertFillScaleContinuousOrNULL`, `assertFillScaleDiscreteOrNULL`.

## basejump 0.3.0 (2018-02-16)

- Switch to using [assertive][] internally for assert checks.
- Now exporting these assert check functions:
  `assert_formal_annotation_col`, `assert_formal_color_function`,
  `assert_formal_compress`, `assert_formal_gene2symbol`,
  `assert_formal_header_level`, `assert_has_rownames`,
  `assert_is_a_number_or_null`, `assert_is_a_string_or_null`,
  `assert_is_an_implicit_integer`, `assert_is_an_implicit_integer_or_null`
  `assert_is_an_integer_or_null`, `assert_is_annotable`,
  `assert_is_character_or_null`, `assert_is_data.frame_or_null`,
  `assert_is_gene2symbol`, `assert_is_implicit_integer`,
  `assert_is_implicit_integer_or_null`, `assert_is_tx2gene`,
  `has_rownames`, `initializeDirectory`, `is_implicit_integer`.
- Renamed `md*` functions to `markdown*`.

## basejump 0.2.1 (2018-02-07)

- Added `convertGenesToSymbols` and `convertTranscriptsToGenes`
  functions. Previously some of this functionality was contained within the
  `gene2symbol` and `tx2gene` generics for the character method. This
  behavior was inconsistent with `gene2symbol` and `tx2gene` usage in the
  [bcbio][] R packages, so I decided to split these out into separate functions.
  Now `gene2symbol` and `tx2gene` work consistently with the `annotable`
  function to return gene-to-symbol and transcript-to-gene identifier mappings
  in a `data.frame`.
- `markdownHeader`, `markdownList`, and `markdownPlotlist` are now
  exported as S4 generics. The `md*` function variants are now exported as
  aliases.
- `geomean` has been renamed to `geometricMean`.
- Miscellaneous improvements to error messages and warnings.

## basejump 0.2.0 (2018-01-28)

- Offloaded internal [bcbio][]-specific code to new package named [bcbioBase][].
  Consequently, this makes the [basejump][] package leaner, meaner, and easier
  to manage. The following functions are now exported in that package:
  `bcbio`, `checkInterestingGroups`, `flatFiles`, `interestingGroups`,
  `metrics`, `plotDot`, `plotGene`, `plotQC`, `plotViolin`,
  `prepareSummarizedExperiment`, `prepareTemplate`, `readDataVersions`,
  `readLogFile`, `readProgramVersions`, `readSampleMetadataFile`,
  `sampleMetadata`, `sampleYAML`, `sampleYAMLMetadata`,
  `sampleYAMLMetrics`, and `selectSamples`. These functions are now
  deprecated here in [basejump][] (see `deprecated.R` file for more
  information).
- `comp` and `revcomp` have been deprecated in favor of `complement`
  and `reverseComplement` from the [Biostrings][] package.
- Internally, errors, messages, and warnings now use methods from the
  [rlang][] package: `abort`, `inform`, and `warn`, in place of `stop`,
  `message`, and `warning`, respectively.
- Improved error handing for missing files in `loadData`. Additionally, the
  file name must match the internal name in the RData file, otherwise
  `loadData` will warn the user. This is more strict than the default
  behavior of `base::load`, but helps prevent accidental overwrite in the
  current working environment.
- `localOrRemoteFile`, previously an internal function, is now exported.
- `annotable` now uses internal [GRCh37][] annotations from the [annotables][]
  package, which is saved in the `extdata/` directory internally. Previously,
  these genome annotations were accessed from lazy loaded data saved in the
  `data/` directory of the package repository.
- `annotables` now checks for all packages attached by [ensembldb][] and
  [AnnotationHub][] and forces detachment at the end of the function call.
  Otherwise, this can result in the unwanted effect of [ensembldb][] masking
  other user-loaded functions, such as the [tidyverse][] suite (e.g.
  `dplyr::select`).
- Consistently reformatted code indents to be a multple of 4 spaces, as
  recommended by [Bioconductor][].
- `camel` now handles delimited numbers a little differently. Previously,
  delimiters in between numbers (e.g. the commas in "1,000,000") were stripped.
  Sometimes this can result in confusing names. For example, if we have a
  column formatted in dotted case containing a decimal (e.g. "resolution.1.6"),
  the decimal would be stripped (e.g. "resolution16" in camel). Now, we
  sanitize a numeric delimiter as a lower case "x" character (e.g.
  "resolution1x6"). This ensures that numbers containing decimals remain
  semantically meaningful when sanitized with `camel`.
- Internally, `gsub` (and `grepl`) calls have been simplified to use the
  default order of "pattern, replacement, x".
- Internally, all implicit integers have been converted to explicit integers,
  where applicable.

## basejump 0.1.10 (2017-12-20)

- Bug fix for multiplexed sample input into `readSampleMetadataFile`. We
  were detecting the presence of `index` column but should instead check
  against `sequence` column.
- Added `dynamicPlotlist` and `mdPlotlist` plotting utilities.
- Added `uniqueSymbols` parameter to `annotable` function.

## basejump 0.1.9 (2017-12-18)

- Added `plotHeatmap` functionality.
- Migrated `tpm` generic from [bcbioRNASeq][], for future use in
  [bcbioSingleCell][].
- Added matrix method support for `plotHeatmap`.
- Added matrix method support for `plotQuantileHeatmap`, which works
  similarly as `plotHeatmap`.

## basejump 0.1.8 (2017-12-14)

- Improved `matrix` and `dgCMatrix` method support in `aggregateReplicates`
  and `aggregateFeatures` functions. Both of these functions now use a
  consistent `groupings` parameter, which uses a named factor to define the
  mappings of either samples (columns) for `aggregateReplicates` or
  genes/transcripts (rows) for `aggregateFeatures`.
- Update for `makeNames` sanitization functions. Now they will work on
  `names(x)` for vectors by default.
- Improved `detectOrganism` to match against "H. sapiens", etc.
- Added internal [GRCh37][] transcript to gene mapping.
- Improved organism matching to detect "Homo_sapiens" and "H. sapiens".
- Factors are now supported in the `makeNames` utilities: `camel`,
  `dotted`, `snake`, and `upperCamel`.
- Improved handling of `NA` values from [LibreOffice][] and
  [Microsoft Excel][Excel] output in `readFileByExtension`. This function now
  sets `""`, `NA`, and `#N/A` strings as `NA` correctly.

## basejump 0.1.7 (2017-12-11)

- Renamed `fc2lr` to `foldChangeToLogRatio` and `lr2fc` and
  `logRatioToFoldChange`.
- Moved `plotDot` and `plotViolin` generics here from [bcbioSingleCell][].
- Added internal [GRCh37][] gene annotations.

## basejump 0.1.6 (2017-12-06)

- Moved `microplate` code from the [wormbase][r-wormbase] package here, since
  it's of general interest.

## basejump 0.1.5 (2017-12-05)

- Added `checkAnnotable`, `checkGene2symbol`, `checkTx2gene`, and
  `sanitizeAnnotable` utility functions that will be used in the bcbio R
  packages.

## basejump 0.1.4 (2017-12-04)

- Added `midnightTheme` [ggplot2][] theme. Originally this was defined as
  `darkTheme` in the [bcbioSingleCell][] package, but can be useful for other
  plots and has been moved here for general bioinformatics usage. The theme now
  uses `ggplot2::theme_minimal` as the base, with some color tweaks, namely
  dark gray axes without white axis lines.
- Improve NAMESPACE imports to include `stats::formula` and
  `utils::capture.output`.

## basejump 0.1.3 (2017-12-01)

- `loadData` and `loadDataAsName` now default to `replace = TRUE`. If an
  object with the same name exists in the destination environment, then a
  warning is generated.
- `collapseToString` only attempts to dynamically return the original
  object class on objects that aren't class `data.frame`. I updated this code
  to behave more nicely with grouped tibbles (`grouped_df`), which are a
  virtual class of `data.frame` and therefore can't be coerced using
  `as(object, "grouped_df")`.
- DNA sequence utility functions `comp` and `revcomp` now return `NULL`
  for integers and numerics.
- For `prepareSummarizedExperiment`, added support for dropping `NULL`
  objects in assays list. This is useful for handling output from
  [bcbioRNASeq][] when `transformLimit` is reached. In this case, the `rlog` and
  `vst` matrices aren't generated and set `NULL` in the assays list. Using
  `Filter(Negate(is.null), assays)` we can drop these `NULL` objects and
  prevent a downstream dimension mismatch in the
  `SummarizedExperiment::SummarizedExperiment` call.
- Improved support for multiplexed files in `readSampleMetadataFile`. This
  now checks for a sequence column containing ACGT nucleotides. When those are
  detected, the `revcomp` column is generated. Otherwise this step is skipped.
  This is useful for handling multiplexed sample metadata from 10X Genomics
  [Cell Ranger][] single-cell RNA-seq samples.
- Updated `annotable` function to include nested [Entrez][] identifiers in the
  `entrez` column. This is useful for downstream functional analysis.

## basejump 0.1.2 (2017-11-30)

- Added [bcbio][] `plotQC` generic.
- Added back `toStringUnique` code, which is still in use in the
  [wormbase][r-wormbase] package.
- Added deprecations for `summarizeRows` (now `collapseToString`) and
  `wash` functions.
- Updated installation method to include manual installation of [ensembldb][].
  Otherwise, [basejump][] installation fails due to [GenomeInfoDb][] and
  [GenomeInfoDbData][] not getting installed completely.
- Now suggesting that the user installs suggested packages in the README.
- Updated [PANTHER][] annotation scripts.
- Bug fix for `detectOrganism`. Now allowing `NULL` return for unsupported
  organism, with a warning.

## basejump 0.1.1 (2017-11-11)

- Added overwrite support for `saveData`. Now will skip on existing files
  when `overwrite = FALSE`.
- Bug fix for `readDataVersions`, which shouldn't have the column types
  defined, using `col_types = "ccT"`.
- Improved key value pair method for `loadDataAsName`. Now rather than
  using a named character vector for the `mappings` argument, the user can
  simply pass the key value pairs in as dots. For example, `newName1 =
  "oldName1", newName2 = "oldName2"`. The legacy `mappings` method will still
  work, as long as the dots argument is a length of 1.
- [Ensembl][] release version now defaults to `NULL` instead of `current` for
  `annotable`, `gene2symbol`, `symbol2gene` and `tx2gene` functions.
- Allow `rowData` to be left unset in `prepareSummarizedExperiment`. This is
  useful for setting up objects that don't contain gene annotations.
- Removed sample selection by pattern matching (`pattern`, `patternCol`
  arguments) in `readSampleMetadata`. This feature wasn't fully baked and
  doesn't offer enough functionality to the user.

## basejump 0.1.0 (2017-10-23)

- Bump version to match [bcbioRNASeq][] package.
- Improved unit testing coverage of `prepareSummarizedExperiment`.
- Added quiet mode support to functions that output messages, where applicable.
- Consolidated [roxygen2][] function imports to `basejump-package.R` file.
- Deprecated `sampleDirs` generic.
- Improved organism detection in `detectOrganism` and added support for
  chicken genome.
- Clarified warning messages in `prepareSummarizedExperiment` to make
  sample loading with `loadRNASeq` and `loadSingleCell` in the [bcbio][]
  packages less confusing.
- Improved `NULL` returns in `readDataVersions`, `readLogFile`, and
  `readProgramVersions` utility functions.
- Fixed export of `*GTF` alias functions to simply wrap the `*GFF`
  functions with S4 methods support.
- Improved lane split technical replicate handling in
  `readSampleMetadataFile`.
- Improved `camel` syntax for both lax and strict modes. Added
  `upperCamel` function.
- Switched `str_` to base `grep` and `gsub` in internal functions.

## basejump 0.0.25 (2017-10-13)

- Improved consistency of `setMethod` calls using `signature`.
- Converted `loadRemoteData` to a standard function instead of using S4
  dispatch, allowing the `envir` argument to be set properly.

## basejump 0.0.24 (2017-10-10)

- Added additional package version requirements in `DESCRIPTION` file.
- Implicit integers are allowed.
- Using [GitHub][] version of [covr][] package for unit tests.
- Renamed `multiassignAsNewEnv` to `multiassignAsNewEnvir`
- Added `*GFF` function variants for `gene2symbolFromGTF` and
  `tx2geneFromGTF`.
- Added shared [bcbio][] generic functions: `aggregateReplicates`, `bcbio`,
  `bcbio<-`, `interestingGroups`, `metrics`, `plotGene`,
  `sampleDirs`, `sampleMetadata`, `selectSamples`. These functions are
  saved in `bcbioGenerics.R` file.
- Incorporated [bcbio][] utility functions shared across [bcbioRNASeq][] and
  [bcbioSingleCell][]: `readDataVersions` (deprecated `.dataVersions`),
  `readLogFile` (deprecated `.logFile`), `readProgramVersions`
  (deprecated `.programs`), `sampleYAML` (deprecated `.sampleYAML`),
  `sampleYAMLMetadata` (deprecated `sampleYAMLMetadata`),
  `sampleYAMLMetrics` (deprecated `.sampleYAMLMetrics`).
- Deprecated `metadataTable` function.
- Moved all [roxygen2][] documentation to `methods-*.R` files where applicable.
- Now using `assays` in `prepareSummarizedExperiment` generic definition as
  primary object.
- Improved `assignAndSaveData` to add silent return of file path.
- Now consistently using clear function definitions in chain operations with
  magrittr pipe (`%>%`).
- Added `.prepareSampleMetadata` utility function, for use with loading
  sample metadata from an external CSV, [Excel][], or YAML file.
- Added `loadData` functionality back to the package.
- Initial commit of `loadDataAsName` function.
- Improved `annotable` function documentation and support for [Ensembl][]
  release versions.
- Improved sanitization rules for `camel`, `dotted`, and `snake` name
  functions. Added the `strict` argument to `camel` and `dotted`.
- Improved the documentation for the `makeNames` functions, by splitting each
  into their own separate methods file.
- Improved S4 method support for the logRatio functions.
- Added integer support for `geomean` function. Also improved internal code
  of `geomean` based on Paul McMurdie's Stack Overflow post. See function
  documentation for more information.
- Added release support for `tx2gene` functions.
- Reduced the number of reexported functions (for documentation) down to the
  [magrittr][] pipe (`%>%`), `Matrix`, `DataFrame`, and `tibble`.
- Added silent return of file path to `saveData` function.
- Improved documentation for [tibble][] coercion using `as(object, "tibble")`
- Renamed `collapse` function to `collapseToString`, to avoid NAMESPACE
  collisions with tidyverse packages ([dplyr][], [glue][]).

## basejump 0.0.23 (2017-09-14)

- Upgraded `annotable` function to query [Ensembl][] using the [ensembldb][]
  package rather than [annotables][].

## basejump 0.0.22 (2017-09-08)

- Improved unit testing coverage.
- Renamed `prepareSE` to `prepareSummarizedExperiment`. Improved row and
  column name handling in the function. It now outputs more helpful diagnostic
  messages on error.
- Reworked and simplified `detectHPC` function to allow for unit testing.

## basejump 0.0.21 (2017-09-01)

- NAMESPACE improvements. Reduced the number of re-exported functions to
  simplify the package.
- Improved code coverage and unit testing with additional [testthat][]
  checks. Specifically, added unit testing for remote download functions and
  improved testing for GTF file utilities.
- Code coverage now above 90%!
- Renamed `packageSE` to `prepareSE` for better semantic meaning.
- Made multiple generics more flexible by inclusion of passthrough (`…`).
- Reduced the number of deprecated functions.
- Initial commit of internal `localOrRemote` utility function.
- Initial commit of `prepareTemplate` function.
- Added additional `data-raw/` scripts.
- Added `onLoad.R` script back to ensure proper attachment of [annotables][]
  data package.
- Removed [tidyverse][] S4 method support.
- Improved remote file handling for `readFileByExtension`, `readGTF`, and
  `readYAML` functions.

## basejump 0.0.20 (2017-08-16)

- Offloaded [devtools][] functions to personal package.
- Upgraded all functions to S4 functions where possible.
- Assign utilities were kept as S3 functions since S4 dispatch makes
  `parent.frame` assignment not work correctly.
- Deprecated snake case and British spelling variants to reduce the number of
  exported functions.
- Added more working examples.
- Added unit testing for [annotables][] functions.

## basejump 0.0.19 (2017-07-24)

- Improved documentation and consistency with [bcbio][] packages.
- Improved integration of gene annotation calls using [annotables][] package.

## basejump 0.0.18 (2017-07-24)

- Initial support for [SummarizedExperiment][] creation with `packageSE`.

## basejump 0.0.17 (2017-07-11)

- Added [annotables][] common code from [bcbio][] packages.
- Added automatic file reading using [readr][] package.
- Combined write counts functions from [bcbioRNASeq][] and [bcbioSinglecell][].
- Initial commit of `assign_data` for use in [bcbioSingleCell][] sample loops.

## basejump 0.0.16 (2017-06-28)

- Minor NAMESPACE updates while working on [bcbio][] packages.
- Tweaks for [tidyverse][] S4 generic verbs. In particular, `as_tibble` now
  provides better consistency for rowname conversion.

## basejump 0.0.15 (2017-06-18)

- Added [testthat][] support for [lintr][] checks.
- Added S4 generic for `as_tibble`.

## basejump 0.0.14 (2017-06-13)

- [dplyr][] 0.7 NAMESPACE fixes and function tweaks.

## basejump 0.0.13 (2017-06-12)

- `setMethod` for [tidyverse][] NAMESPACE collisons ([dplyr][], [tidyr][])
  using `signature("data.frame")`.

## basejump 0.0.12 (2017-05-25)

- Updated exports based on [wormbase][r-wormbase] package.

## basejump 0.0.11 (2017-05-18)

- Improved naming functions to dynamically handle character vectors and objects
  that support naming assignments.
- Added `removeNA` utility function.

## basejump 0.0.10 (2017-05-14)

- Added NAMESPACE utilities to deal with [tidyverse][] generic verbs.
- Switched package documentation method to use [roxygen2][] with pkgapi.

## basejump 0.0.9 (2017-05-13)

- Added snake case function variants.

## basejump 0.0.8 (2017-05-13)

- Added back `saveData` utility functions.

## basejump 0.0.7 (2017-0422)

- Bug fixes for [dplyr][] 0.6.0 update and improved kable handling.

## basejump 0.0.6 (2017-04-14)

- Dependency fix for successful compilation on the [HMS RC][] Orchestra cluster.

## basejump 0.0.5 (2017-04-12)

- Consolidated functions in the documentation.

## basejump 0.0.4 (2017-04-07)

- Improved documentation.

## basejump 0.0.3 (2017-03-22)

- Removed dependencies and transfer functions to [bcbioRNASeq][].

## basejump 0.0.2 (2017-03-22)

- Added [bcbio][] data import functions.
- Added [ggplot2][] wrapper functions for quality control.

## basejump 0.0.1 (2017-03-17)

- Initial draft release.

[acid genomics]: https://acidgenomics.com/
[acidbase]: https://acidbase.acidgenomics.com/
[acidplots]: https://acidplots.acidgenomics.com/
[annotables]: https://github.com/stephenturner/annotables/
[annotationhub]: https://bioconductor.org/packages/AnnotationHub/
[appveyor ci]: https://ci.appveyor.com/
[assertive]: https://cran.r-project.org/package=assertive
[basejump]: https://basejump.acidgenomics.com/
[bb8]: https://bb8.acidgenomics.com/
[bcbio]: https://github.com/bcbio/bcbio-nextgen/
[bcbiobase]: https://bioinformatics.sph.harvard.edu/bcbioBase/
[bcbiornaseq]: https://bioinformatics.sph.harvard.edu/bcbioRNASeq/
[bcbiosinglecell]: https://bioinformatics.sph.harvard.edu/bcbioSingleCell/
[biocinstaller]: https://bioconductor.org/packages/BiocInstaller/
[biocmanager]: https://cran.r-project.org/package=BiocManager
[bioconductor]: https://bioconductor.org/
[biostrings]: https://bioconductor.org/packages/Biostrings/
[bioverbs]: https://bioverbs.acidgenomics.com/
[brightworm]: https://brightworm.acidgenomics.com/
[brio]: https://brio.acidgenomics.com/
[cell ranger]: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
[checkmate]: https://cran.r-project.org/package=checkmate
[conda]: https://conda.io/
[covr]: https://cran.r-project.org/package=covr
[cran]: https://cran.r-project.org/
[data.table]: https://cran.r-project.org/package=data.table
[devtools]: https://cran.r-project.org/package=devtools
[dplyr]: http://dplyr.tidyverse.org/
[eggnog]: http://eggnogdb.embl.de/
[ensembl]: https://www.ensembl.org/
[ensembldb]: https://bioconductor.org/packages/ensembldb/
[entrez]: https://www.ncbi.nlm.nih.gov/Web/Search/entrezfs.html
[excel]: https://products.office.com/en-us/excel/
[freerange]: https://freerange.acidgenomics.com/
[genomeinfodb]: https://bioconductor.org/packages/GenomeInfoDb/
[genomeinfodbdata]: https://bioconductor.org/packages/GenomeInfoDbData/
[ggplot2]: http://ggplot2.tidyverse.org/
[github]: https://github.com/
[glue]: https://glue.tidyverse.org/
[goalie]: https://goalie.acidgenomics.com/
[grch37]: https://grch37.ensembl.org/
[hgnc]: https://www.genenames.org/
[hms rc]: https://rc.hms.harvard.edu/
[koopa]: https://koopa.acidgenomics.com/
[libreoffice]: https://www.libreoffice.org/
[lintr]: https://github.com/jimhester/lintr/
[macos]: https://www.apple.com/macos/
[magrittr]: https://magrittr.tidyverse.org/
[markdown]: https://daringfireball.net/projects/markdown/
[mgi]: http://www.informatics.jax.org/
[nih]: https://www.nih.gov/
[panther]: http://pantherdb.org/
[pheatmap]: https://cran.r-project.org/package=pheatmap
[pointillism]: https://pointillism.acidgenomics.com/
[r-wormbase]: https://wormbase.acidgenomics.com/
[r]: https://www.r-project.org/
[readr]: http://readr.tidyverse.org/
[rio]: https://cran.r-project.org/package=rio
[rlang]: http://rlang.tidyverse.org/
[roxygen2]: https://cran.r-project.org/package=roxygen2
[s4vectors]: https://bioconductor.org/packages/S4Vectors/
[summarizedexperiment]: https://bioconductor.org/packages/SummarizedExperiment/
[syntactic]: https://syntactic.acidgenomics.com/
[testthat]: https://cran.r-project.org/package=testthat
[tibble]: https://tibble.tidyverse.org/
[tidyr]: http://tidyr.tidyverse.org/
[tidyverse]: http://www.tidyverse.org/
[transformer]: https://transformer.acidgenomics.com/
[travis ci]: https://travis-ci.com/
[ucsc]: https://genome.ucsc.edu/
[windows]: https://www.microsoft.com/en-us/windows/
[wormbase]: http://www.wormbase.org/
