SmartR 1.2 Stable Release

NEW [IPAConnector]

• Please contact [email protected] for any questions

NEW [PatientMapper Workflow]

• Enables the user to modify the cohort to reflect the same patient set but in a different study

[Boxplot Workflow]

• The user can now create groups by using categorical variables

[Heatmap Workflow]

• Fixed a bug related to sample sorting

SmartR 1.1 Stable Release

Changelog

The changelog might be incomplete. This release contains over 200 commits, which add over 15.000 LOC, that affect 43 files, so I might have forgotten a thing or two.

Installation Instructions

[General]

• [Enhancement] Improved speed for on-the-fly computations if many files have been loaded

NEW [Timeseries Workflow]

• [Feature] Support for numerical, categorical and high dimensional time series data
• [Feature] Re-arrangeable time axis
• [Feature] Time axis evenly spaced or in relation to other time points
• [Feature] Switch between different error measures and statistics to summarise patients
• [Feature] Compute mean and standard deviation on-the-fly for any timeline
• [Feature] Rank categorical time series data manually and display most significant patients
• [Feature] Smooth timelines on-demand
• [Feature] Several hover and tooltip features

[Boxplot Workflow]

• [Feature] The workflow is now based on plotly.js
• [Feature] High dimensional data support

SmartR 1.0 Stable Release

Changelog

This is the first stable release for SmartR.

An upgrade is recommended but not strictly necessary if you don't experience any issues with the RC release. Installation Instructions

[General]

• [Bug] Fixed issue where user was redirected to Grails welcome page, rather than the TM interface (Thanks @anthony-o )
• [Bug] Correctly read port variable for Rserve server from configuration file
• [Improvement] Improved compatibility with 16.2 & eTRIKv3 builds
• [Improvement] Added "Capture" button to each workflow
• [Improvement] Moved workflow controls to avoid collision with browser scrollbar
• [Misc] Test cases fixed

[Heatmap Workflow]

• [Improvement] Downloaded data now match data table
• [Bug] Fixed several issues concerning time series HDD data
• [Bug] Fixed API calls for pathway enrichment analysis via Biocompendium

SmartR 1.0 Release Candidate

Changelog

Note: This list highlights the most visible changes. "Under the hood" much more happened, such as the performance improvements, code cleanups/refactorings or small visual changes, for example a more consistent font sizing in the heatmap. A list of all 46 closed issues can be found >>here<<
An upgrade to this version is highly recommended: Installation instructions

[General]

• [Feature] Possibility to return and display R warnings in WF
• [Improvement] Massively improved ergonomy of all workflows, e.g.
  better tooltips, better contextmenues, better control placements
• [Improvement] Use subjectID rather than transmartID
• [Improvement] Many checks have been added to prevent launching a WF
  with wrong input, e.g. HDD nodes of different platform
• [Bug] Fixed bug that could prevent InternetExplorer from fetching
  data
• [Bug] Fixed bugs around incorrect placement of contextmenu and
  other issues linked to it
• [Bug] Errors are now properly shown, rather than having silent crashing and
  endless fetching or the kind

[Heatmap Workflow]

• [Feature] Low dimensional data support
• [Feature] On-the-fly change of displayed significance criteria,
  e.g. mean, variance, log fold change, ...
• [Feature] Table displaying all possible ranking statistics,
  dynamically linked to the heatmap sorting
• [Improvement] Consistent naming according to node label, e.g. 1000123_BreastCancer_s2
• [Improvement] Visual indication of chosen sorting
• [Bug] Fixed bug that caused old summary stats to be displayed

[Boxplot Workflow]

• [Feature] log transformation of data by choice

[Correlation Workflow]

• [Feature] log transformation of data by choice

[Volcanoplot Workflow]

• [Feature] Ported workflow to Angular and made it functional
  again

Second beta for 1.0 release

Changelog:

• General: Completley new tooltip and context menu design and behaviour
• Heatmap: (Re-)added EMBL EBI and GeneCards links to feature names
• Heatmap: Subsets are not swapped anymore in summary statistics
• Correlation: Fixed bug where histograms where too big
• Concept box is now scrollable
• Data cannot be fetched anymore if input is invalid
• Moved SmartR tab next to Advanced workflow
• Many little design and user experience improvements
• Total list of resolved issues: https://jira.transmartfoundation.org/projects/SH/versions/11005

First beta for 1.0 release

No change log behind this point