# DeeDeeExperiment 1.2.0

* The `dea` and `fea` slots now use `S4Vectors::SimpleList` instead of base `list`

* The DEA original objects are no longer stored in the `dea` slot. They are now
stored under `metadata(dde)$singlecontrast` or `metadata(dde)$multicontrast`, and
each contrast entry in the dea slot contains a pointer to its original object

* Added helper functions to simplify inserting DE results from `muscat::pbDS()`
and `MArrayLM` object with multiple contrast into a `dde` object

* Added a helper function to export results stored in `dea` and `fea` slots as
excel files

* Improved warning messages

* A new vignette showcasing how to apply `DeeDeeExperiment` to a single-cell
dataset

* Updating citation since the `DeeDeeExperiment` paper is out!

# DeeDeeExperiment 1.0.0

`DeeDeeExperiment` is now on Bioconductor!

# DeeDeeExperiment 0.99.5

* Addressing final comments for the Bioc review

# DeeDeeExperiment 0.99.4

* Addressing more points related to the Bioc review, mainly adopting camelCase
naming for generics & methods

# DeeDeeExperiment 0.99.2

* Addressed the points raised in the Bioc review

* Expanded the supported DEAs (as simple `data.frame` object that contains
at least three columns named `log2FoldChange`, `pvalue`, and `padj`)

# DeeDeeExperiment 0.99.1

* `DeeDeeExperiment` now extends the `SingleCellExperiment` class, accommodating
both bulk and single-cell analysis workflows

* Ready for Bioconductor review!

# DeeDeeExperiment 0.99.0

* Ready for Bioconductor submission!

# DeeDeeExperiment 0.6.0

* Full vignette now available for user guidance

# DeeDeeExperiment 0.5.0

* Reducing the dependency stack to make the class/package as slim as it can be,
with a focus on the full interoperability with SE (therefore now a full dependency)

# DeeDeeExperiment 0.4.0

* New methods to rename DEA and FEA elements in `dde` objects, get all FEAs for
a specific DEA, assign DEA to FEA

* Method dispatch is now only base on x being `DeeDeeExperiment`, other arguments
are no longer part of the method signature

* Expanded supported FEAs: now takes results from `topGO`, `clusterProfiler`,
`enrichR`, `gProfiler`, `fgsea`, `gsea`, `DAVID`, and output of `GeneTonic` shakers

# DeeDeeExperiment 0.3.0

## New features

* Methods to retrieve and manage the `fea` slot content are established

* supported FEAs: topGO (data.frame) & enrichResult objects

* A summary method is included to provide a quick overview of stored DEA and
FEA results

# DeeDeeExperiment 0.2.0

## New features

* `dea()` has been refactored for clarity:
  - Now it returns only the main results table, acting as `get_dea_df()`
  - A new function, `dea_info()`, has been added to return additional information
  previously returned by `dea()`

* Initial implementation of the `fea` slot

# DeeDeeExperiment 0.1.0

## New features

* The `DeeDeeExperiment` class is now being developed in its own standalone
package, following its separation from the original `DeeDee_legacy` repository:
https://github.com/imbeimainz/DeeDee_legacy
