Changes in version 1.7.0                        

We add the following function:

  - enrichedIn: This function generates a binary matrix in which the
    rows represent GO terms, and the columns represent lists. The matrix
    uses the values TRUE or FALSE to indicate whether each GO term is
    enriched or not for each list.

In addition:

  - We have updated the buildEnrichedTable and allBuildEnrichedTable
    functions. They now uses the outcomes of enrichedIn to build the
    contingency table. During the conducted tests, the speed of the
    procedure for generating contingency tables increased by a factor of
    six compared to the previous version.
    
    Furthermore, we have included the showEnrichedIn argument in these
    functions. This is a boolean argument. If the argument is TRUE, in
    addition to the enrichment contingency table, the function saves a
    matrix in the global environment, which contains the cross table of
    the enriched and non-enriched GO terms vs the names of the gene
    lists generated with the enrichedIn function. This matrix is stored
    under the name of "enrichedIn_" followed by the name of the ontology
    and the level being analysed. An object will be produced for every
    scenario if there are several levels and ontologies.

  - We add the vignette "irrelevance-threshold_Matrix_Dissimilarities."
    This vignette illustrates calculating, visualizing, and interpreting
    the irrelevance-threshold matrix of dissimilarities D. This matrix
    provides dissimilarities between pairs of compared lists. These
    dissimilarities are not only a descriptive measure but also based on
    the irrelevance threshold determining whether two lists are
    equivalent. So, this dissimilarity measure between the two lists is
    directly associated with their declaration of equivalence.
    
    The matrix D can be represented in interpretable statistic graphs
    such as dendrograms or biplots, which help to visualize the
    formation of groups containing equivalent lists. Furthermore,
    interpreting the biplot dimensions gives us the biological functions
    responsible for the equivalence between lists.

                        Changes in version 1.3.0                        

We add the following functions:

  - allBuildEnrichTable: This function produces k(k–1)/2 contingency
    tables by comparing all possible pairs of feature lists using the
    provided GO ontologies and GO levels.
  - allEquivTestSorensen: This function computes the k(k–1)/2
    equivalence tests by comparing all possible pairs of feature lists
    using the provided GO ontologies and GO levels.
  - sorenThreshold: This function applies an algorithm to compute the
    irrelevance-threshold matrix of dissimilarities for a specific
    ontology and GO level.
  - allSorenThreshold: This function iterates sorenThreshold along the
    specified GO ontologies and GO levels
  - hclustThreshold: This function plots a dendrogram for a specific
    ontology and GO level based on the irrelevance-threshold matrix of
    dissimilarities..
  - allHclustThreshold: This function iterates hclustThreshold along the
    specified GO ontologies and GO levels

In addition:

  - We enhance the vignette "An introduction to the goSorensen package"
    by incorporating the newly introduced functions and updating the
    example results with the latest version of Bioconductor.

                        Changes in version 1.2.0                        

  - Added some results (allTabsBP.4 object) about computed crosstabs for
    all possible list pairs in allOncoGeneLists for BP ontology, level 4

                        Changes in version 1.1.0                        

  - This is the first version submitted to review. There are currently
    no updates.