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Changelog

Source: NEWS.md

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

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