NEWS.md

In GeneTonic: Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

GeneTonic 1.2.0

New features

• The geneset distillery is officially open! GeneTonic offers functionality to aggregate together gene sets into overarching biological themes, based on a network-based refinement of the enrichment map. Corresponding graphical functionalities are also extended to accommodate meta-genesets. An efficient implementation for the Markov clustering on graph objects is also provided

• GeneTonic can now receive the input of many other tools for functional enrichment analysis - this includes the output (text export) of DAVID (shake_davidResult), enrichr (from website and via the package, with shake_enrichrResult), fgsea (shake_fgseaResult), and g:Profiler (with shake_gprofilerResult, which can handle the textual output from the website, as well the one from the call to the gost in gprofiler2)

• An export button to a SummarizedExperiment object for iSEE and its underlying machinery has been added. If the visualization options in GeneTonic are not exactly what you would expect, you might find an excellent venue in the iSEE framework

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safe fails when not finding the GO Term and searching for the definition - this could happen e.g. when the term becomes outdated and is removed from the GO.db package, or also mistyped if entered by hand at some point.
• gs_heatmap has a new parameter, plot_title, to override the title to be displayed and set it to any custom string
• It is now possible to save a snapshot of the graphs created with visNetwork
• The Gene Box now also contains links to the GTEx portal for the selected feature
• export_to_sif enables to export a graph object to a text file, encoded with the SIF format

GeneTonic 1.0.0

Other notes

• GeneTonic has become a part of Bioconductor!

GeneTonic 0.99.0

Other notes

• GeneTonic is now submitted to Bioconductor!

GeneTonic 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!

GeneTonic 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

GeneTonic 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

GeneTonic 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

GeneTonic 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

GeneTonic 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.

GeneTonic 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

GeneTonic 0.3.0

Other notes

• Rearranging the order of parameters to harmonize it across functions, and uniforming similarly called parameters

GeneTonic 0.2.0

New features

• added geneset scoring calculation and corresponding heatmap

GeneTonic 0.1.0

New features

• much of the functionality available, in a proof of concept format

GeneTonic 0.0.1

New features

• backbone of the project started!

GeneTonic documentation built on Nov. 8, 2020, 5:27 p.m.