## Changes in version 1.26.0

### Bug fixes and minor improvements

* Replaced local pull request workflow with reusable GitHub Actions wrapper
* Updated author, contributor, and funding metadata in `DESCRIPTION` and
  `CITATION.cff`
* Trimmed unnecessary software references from `CITATION.cff`

## Changes in version 1.22.0

### Bug fixes and minor improvements

* Updated vignette authorship information
* Added sticker to `README.md`
* Enhancements to GitHub Actions workflows

## Changes in version 1.20.0

### Bug fixes and minor improvements

* Minor fixes to documentation and imports in `NAMESPACE`.
* Use Markdown in documentation.

## Changes in version 1.18.0

### Bug fixes and minor improvements

* Added `CITATION.cff` file to the package and note in the `DESCRIPTION` file.

## Changes in version 1.16.0

### New features

* Added citation information to the package; see
`citation("SingleCellMultiModal")` and the vignette.

### Bug fixes and minor improvements

* Update imports from `SingleCellExperiment`, `S4Vectors`, and
`SummarizedExperiment`
* Add package anchors to links in documentation
* Use markdown in documentation

## Changes in version 1.14.0

### New features

* The `ontomap` function provides a reference table of ontology IDs and cell
names by data type available in the package.
* `scRNAseq` `colData` added to `cord_blood` and `peripheral_blood` datasets
provided by the `CITEseq` function. (@drighelli)

### Bug fixes and minor improvements

* When using `HDF5` as `format` input in `scMultiome`, the filtering of file
paths obtained from `ExperimentHub` has been fixed.
* Using `BiocBaseUtils` internally to handle assertions and checks.

## Changes in version 1.12.0

### Bug fixes and minor improvements

* Added Ludwig Geistlinger as author (@lgeistlinger) for contributing the
`GTseq` dataset.

## Changes in version 1.8.0

### Bug fixes and minor improvements

* Updated the reference in the `SCoPE2` vignette (@cvanderaa).

## Changes in version 1.6.0

### New features

* `scMultiome` version `1.0.1` provides the 10X format for RNAseq data.

### Bug fixes and minor improvements

* Updates to `seqFISH` vignette and documentation.
* Updated to changes in `SummarizedExperiment` where `assayDimnames` are
checked.
* `scNMT` defaults to version '1.0.0's QC filtered cells. For unfiltered
cells see version section in `?scNMT`.

## Changes in version 1.4.0

### New features

* `SingleCellMultiModal` function allows the combination of multiple
multi-modal technologies.
* `GTseq` data from Macaulay et al. (2015) now available (@lgeistlinger)
* `SCoPE2` data from Specht et al. now available thanks to @cvanderaa (#26)
* `scMultiome` provides PBMC from 10X Genomics thanks to @rargelaguet

### Bug fixes and minor improvements

* Metadata information (function call and call to technology map) included in
`SingleCellMultiModal`
* `scNMT` includes the original call in the `MultiAssayExperiment` metadata
* Improved and edited Contributing Guidelines for clarity
* `seqFISH` uses the `spatialData` argument with `DataFrame` input based on
changes to `SpatialExperiment` (@drighelli)
* Removed the extra column in the `sampleMap` in `CITEseq` (@drighelli)

## Changes in version 1.2.0

### New features

* `CITEseq` function, vignette, and 'cord_blood' data available
(@drighelli, #18)
* Include `seqFISH` function, vignette, and 'mouse_visual_cortex' data
(v1 and v2 from @drighelli, #14)
* New 'mouse_gastrulation' dataset released (version "2.0.0").
* Use `version` argument to indicate the `mouse_gastrulation` data version
* The data includes **all** cells not only the ones that passed the QC
of all three 'omics (thanks @rargelaguet, @ajabadi).

### Bug fixes and minor improvements

* Caching mechanism uses `tools::R_user_dir` and not `rappdirs`.
* Improved display of available data using `ExperimentHub` metadata.
* Improved documentation explaining versioning differences.
* Contribution guidelines available at
https://github.com/waldronlab/SingleCellMultiModal/wiki/Contributing-Guidelines
* Default `version` argument in `scNMT` function now set to "2.0.0" (version
"1.0.0" still available)

## Changes in version 1.0.0

### New features

* `scNMT` serves the mouse gastrulation dataset from Argelaguet et al. 2019
* Data set is provided by Argelaguet and colleagues via CloudStor link:
https://cloudstor.aarnet.edu.au/plus/s/Xzf5vCgAEUVgbfQ
* GitHub repository for the dataset by the authors available at:
https://github.com/rargelaguet/scnmt_gastrulation

### Bug fixes and minor improvements

* Row names in the scNMT dataset properly show mouse ENSEMBL identifiers
