Changes in version 1.18.0
Bug fixes
- Fixed the unexpected behaviour when decorating the signature heatmap
with colData elements
Other notes
- 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
Changes in version 1.16.0
New features
- 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.
Other notes
- The manuscript of ideal is now published in BMC Bioinformatics! The
citation file has been updated accordingly.
- A full round of styler has been applied to the codebase.
Changes in version 1.14.0
Other notes
- Replaced dependency from d3heatmap with the functionality of
heatmaply
- 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 via showNotification
- The vignette and the tour contain a section about the format
required to run ideal correctly
- 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 fgsea or gprofiler2
Changes in version 1.12.0
New features
- Implemented a series of gentle fail mechanisms to avoid abrupt
crashing of the app if the expected objects or formats are not
provided
Other notes
- 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 the rlog
- The installation information in the README.md includes 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
Changes in version 1.10.0
New features
- ggplotCounts gains 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
Bug fixes
- Fixed an error in the initialization of the app due to a new
behavior introduced by shinyAce in version >= 0.4.0 - occurred in
the same way as for pcaExplorer
Other notes
- Better class checks via is(...) as per BiocCheck suggestion
Changes in version 1.8.0
New features
- plot_ma gains 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 keytypes of the
corresponding annotation packages (which still need to be installed
when ideal is 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
as ENSEMBL are not available, like in Arabidopsis (where ids are
provided often as TAIR) - thanks to Marc Galland for picking this up
in https://github.com/federicomarini/ideal/issues/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 SummarizedExperiment object, which can be seamlessly fed
into iSEE
(http://bioconductor.org/packages/release/bioc/html/iSEE.html). This
leverages a new function, wrapup_for_iSEE, which is available and
exported from ideal.
Other notes
- 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
Changes in version 1.6.0
New features
- 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)
Other notes
- Built project website via pkgdown, with customized reference
structure
- Added a NEWS.md file 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
Bug fixes
- Fixed behavior of rendering inline the content of the report - did
not work properly for server deployed instances
Changes in version 1.4.0
New features
- Specified single go term selection for generating heatmaps of gene
signatures
- Added support for logFC shrinkage, following the latest devels of
DESeq2
Bug fixes
- Corrected output for the vignette, as html_document2 is now
deprecated
- Menus are back in the expanded form
- Fixed the behavior with addMLE
Other notes
- 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
Changes in version 0.99.0
New features
- Ready for Bioc submission
- Completed the news
Changes in version 0.9.1
New features
- Added Instructions fully from rendered version of the vignette to
have available at runtime
- Added support for downloading all plots and tables
Changes in version 0.9.0
New features
- Interactive tours are covering now all tabs, with extensive
walkthroughs for the user
- Added all screenshots to vignette
Changes in version 0.6.2
New features
- Interactive tours are now available, coded in external files
- Travis-CI is now supported
Changes in version 0.6.0
New features
- 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
Changes in version 0.4.0
New features
- Gene box info added, based on rentrez
- New look for MA plots and volcano plots
Changes in version 0.3.0
New features
- Restructuring of the folders done, package can be correctly
installed, loaded - namespace, description are set up
Changes in version 0.2.0
New features
- Correct structure of the package
Changes in version 0.1.0
New features
- Package created!