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 is now on Bioconductor!
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 now extends the SingleCellExperiment class, accommodating
both bulk and single-cell analysis workflows
Ready for Bioconductor review!
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
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
dea() has been refactored for clarity:
get_dea_df()dea_info(), has been added to return additional information
previously returned by dea()Initial implementation of the fea slot
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