- The transition to the functions available in the
mosdefBioconductor is complete, with the original functions now being deprecated. This applies togoseqTable()(now replaced bymosdef::run_goseq()), which has now been made faster and more robust in its functionality and in the ways it can be executed - The gene plot widgets now also use the
gene_plot()function frommosdef, instead of the previousggplotCounts()function -gene_plot()is more flexible and has more options to control the behavior of the final plot object - The
deseqresult2tbl()anddeseqresult2DEgenes()are now replaced by the more flexiblemosdef::deresult_to_df() - The internally defined
createLinkENS(),createLinkGeneSymbol(), andcreateLinkGO()are now replaced by the equivalent functions inmosdef - The Roxygen-based documentation now supports markdown. No visible changes should appear to the user, as the content should have stayed fairly the same
- Although no visible changes for the end user are expected, the incoming major version bump will reflect the change in the dependency graph, ensuring that this is noticed at least at the version numbering level
- Fixed the unexpected behaviour when decorating the signature heatmap with colData elements
- Some alignments of the UI elements in the
ideal()app, to harmonize the content of the page - Updated the icons in the user interface to match recent changes in the names from FontAwesome
- It is now possible to export the processed data (count data, results, functional enrichment table) into a combined list object, which can be seamlessly fed into
GeneTonic(http://bioconductor.org/packages/release/bioc/html/GeneTonic.html). - Adjusted the behavior for the modeling with LRT, with extra notifications to inform the user on how to make the most out of the functionality.
- The manuscript of
idealis now published in BMC Bioinformatics! The citation file has been updated accordingly. - A full round of
stylerhas been applied to the codebase.
- Replaced dependency from
d3heatmapwith the functionality ofheatmaply - Additional notifications are returned when closing the app while saving the state to the R environment - both in the console as a
message, and in the UI viashowNotification - The vignette and the tour contain a section about the format required to run
idealcorrectly - The vignette also indicates some exemplary steps after exporting the values to the R environment, showcasing how to perform additional functional enrichment analyses e.g. via
fgseaorgprofiler2
- Implemented a series of gentle fail mechanisms to avoid abrupt crashing of the app if the expected objects or formats are not provided
- Alignments of UI elements have been adjusted
- Updated citation info - the preprint for
ideal, "ideal: an R/Bioconductor package for Interactive Differential Expression Analysis", is now published at bioRxiv, https://doi.org/10.1101/2020.01.10.901652 - Data transformation (for table viewing and visualizations, where homoscedastic data is expected) is now taken care of with the variance stabilizing transformation (
vst), instead of therlog - The installation information in the
README.mdincludes a troubleshooting section to solve some common issues one might encounter - Added a collapsible element in the Data Setup panel, to remind users to perform proper Exploratory Data Analysis (e.g. with
pcaExplorer) before testing for Differential Expression
ggplotCountsgains a new parameter,labels_repel, to control the placement of the different labels in the plot - this can be useful when a large number of samples is available
- Fixed an error in the initialization of the app due to a new behavior introduced by
shinyAcein version >= 0.4.0 - occurred in the same way as forpcaExplorer
- Better class checks via
is(...)as perBiocChecksuggestion
plot_magains an additional parameter,labels_repel, for better placing the labels on the features to mark- The pairwise correlation plots can now use logarithmic scale in the axes, use smaller subsets of the data for quicker inspection, and resizes the correlation info proportionally to its intensity
- The id types can now be chosen among the
keytypesof the corresponding annotation packages (which still need to be installed whenidealis launched). Other input fields that specify id types also behave in a similar manner (e.g. in the Signature Explorer tab). This caused a problem for scenarios where common id types such asENSEMBLare not available, like in Arabidopsis (where ids are provided often asTAIR) - thanks to Marc Galland for picking this up in #1 - The Signatures Explorer tab also has a fully fledged tour for first-time users, together with a collapsible help panel to describe its functionality in brief
- The zoomed MA-plot gains a new widget to control the labels size for the names of the genes
- It is possible to export the input data together with the results in a combined
SummarizedExperimentobject, which can be seamlessly fed intoiSEE(http://bioconductor.org/packages/release/bioc/html/iSEE.html). This leverages a new function,wrapup_for_iSEE, which is available and exported fromideal.
- An information box has been added to provide detailed information on the required input formats
- Added notification to specify how to install the airway package for demonstration purposes if not already available
- The Signatures Explorer tab is now displayed in a conditional panel, i.e. only when the required inputs are provided
- Added extra diagnostic to results exploration (stratified pvalues histograms, schweder-spjotvoll plot)
- Added functionality for the tab Signatures Explorer: read in gmt files, and explore signatures for all/DE genes visually as heatmaps. The signatures can also be provided in the main call of the function as an argument, on top of uploading at runtime
- Different handling of the selection of ids/gene names, now not requiring anymore that the result is computed, but based on the dds object (and on the presence or not of the annotation object)
- Built project website via pkgdown, with customized reference structure
- Added a
NEWS.mdfile to track changes to the package - Updated the report template as well for including new functionality, and also updated vignette entry
- Correctly adding the resources to shinyBS, loaded via
.onLoad - Replaced the first tour structure and call
- New skin for the app, also with logo in the title header
- Instructions start collapsed for more compact main page
- Edited link in button to provide feedback, with subject specified
- Fixed behavior of rendering inline the content of the report - did not work properly for server deployed instances
- Specified single go term selection for generating heatmaps of gene signatures
- Added support for logFC shrinkage, following the latest devels of DESeq2
- Corrected output for the vignette, as html_document2 is now deprecated
- Menus are back in the expanded form
- Fixed the behavior with addMLE
- Added further progress indicators to give feedback during lengthy steps
- Improved ggplotCounts for better scale display, using exact arg matching, defaulting to the transformed counts
- Ready for Bioc submission
- Completed the news
- Added Instructions fully from rendered version of the vignette to have available at runtime
- Added support for downloading all plots and tables
- Interactive tours are covering now all tabs, with extensive walkthroughs for the user
- Added all screenshots to vignette
- Interactive tours are now available, coded in external files
- Travis-CI is now supported
- Added MA plot with extra custom list to avoid manual selection of many genes
- MA plot function now automatically supports subset of gene to be extra plotted
- Added documentation with roxygen to all functions
- Heatmap functions for genes annotated to a GO term as signature
- Template report also provided
- Full draft of vignette now available, working towards bioc submission
- Added textual help to all sections, with collapsible element
- Added proof of principle to have interactive tours based on rintrojs
- Gene box info added, based on rentrez
- New look for MA plots and volcano plots
- Restructuring of the folders done, package can be correctly installed, loaded - namespace, description are set up
- Correct structure of the package
- Package created!