Changes in version 1.2.0 Other notes - Added an additional mechanism for safe fails when not finding the GO Term and searching for the definition - this could happen e.g. when the term becomes outdated and is removed from the GO.db package, or also mistyped if entered by hand at some point. Changes in version 1.0.0 Other notes - GeneTonic has become a part of Bioconductor! Changes in version 0.99.0 Other notes - GeneTonic is now submitted to Bioconductor! Changes in version 0.10.0 New features - The functions for comparing different res_enrich, namely gs_radar, gs_summary_overview_pair, and gs_horizon were internally rewritten to accept correctly the comparison elements - The vignette now covers completely the usage cases, with the full description of the user interface of GeneTonic - The introductory tours are available for all the main panels of GeneTonic. Feel free to try them out! Other notes - Some widgets have been added in the UI of GeneTonic to enable finer control of the output aspect - Examples and unit tests have been further expanded, with better messages for checking progress - check_colors verify that color palettes are correctly provided - Info on GeneTonic is now provided with modal dialog windows, rather than in a separate tab - The tab names in the main app were slightly edited to better describe their content - The info boxes are now shown with a uniform style, based on the bs4Card UI element - The UI elements have now a better spacing throughout the different tabs - Soon the package will be submitted to Bioconductor! Changes in version 0.9.0 New features - GeneTonic sports a blazing new hex sticker - say bye to the original draft! - The overview DT datatables has some styling with color bars - e.g. for DE results - to enhance the visual perception of numeric values (e.g. log2FoldChange) - gs_heatmap can now take a custom list of gene identifiers (when no geneset is passed) - The color palettes in enrichment maps now respect the values and the range specified of the numeric values to be used for mapping to colors - gs_mds is now optionally returning a data.frame, to be further used for custom plotting or downstream processing - gs_summary_overview now has coloring enabled by the variable of choice Other notes - The UI has received some restyling (e.g. in the choice of the icons for the dropdown menus, or the name of some buttons) - Added tour contents for most of the functionality - Added link to the demo instance - Added examples for overlap functions, gene info buttons, map2color, and deseqresult2df - Extended documentation of some parameters - Some functions have gained an alias for calling them: gs_spider is equivalent to gs_radar, and gs_sankey is equivalent to gs_alluvial Changes in version 0.8.0 New features - GeneTonic now delivers bundled example objects to make examples and tests slim - gs_volcano can now plot points by different colors according to the columns of interest - GeneTonic has a fully fledged manual describing its functionality and user interface Other notes - Now using ids for genes and genesets for exchanging information in the app - Added examples for all functions - Most tabs have working tours - anchor and text elements Changes in version 0.7.0 New features - Introduced a uniform interface for calculating different similarity/distance matrices. This enables the usage in the different functions that might need such matrices for further downstream processing (e.g. enrichment_map(), gs_mds()) - First appearance of gs_dendro() to display distance matrices with some visualization sugar, as an alternative to other methods - The n_gs and gs_ids are exposed to more functions to enable custom subsets of the enrichment results to be inspected Changes in version 0.6.0 New features - gs_heatmap now relies on ComplexHeatmap, to avoid the issues with Shiny of not displaying the outputs in the app, and enabling a comfortable heatmap annotation - Many functions gain the possibility to pass a set of custom geneset identifiers to be added to the top N sets (default): among these, gs_mds, gs_volcano (parameter: gs_labels), gs_alluvial, ggs_network, enrichment_map, and enhance_table (using gs_ids) Other notes - gs_ggheatmap got renamed to gs_scoresheat - The report generated from the bookmarked content is expanded in its default content Changes in version 0.5.0 New features - GeneTonic now enforces a format for res_enrich, and provides some conversion functions, shake_*(). Requirements are specified in the documentation, if an appropriate converter does not (yet) exist. - The reporting feature is active to some extent on the bookmarked content. Changes in version 0.4.0 New features - Added functionality for bookmarking - Bookmarking can work (PoP) by pressing a key (left control)! - gene_plot can enforce a plot type overriding the default based on the number of samples per condition - GeneTonic uses now bs4Dash and many of its nice features, replacing the previous implementation based on shinydashboard Changes in version 0.3.0 Other notes - Rearranging the order of parameters to harmonize it across functions, and uniforming similarly called parameters Changes in version 0.2.0 New features - added geneset scoring calculation and corresponding heatmap Changes in version 0.1.0 New features - much of the functionality available, in a proof of concept format Changes in version 0.0.1 New features - backbone of the project started!