Changelog

PanHunter v25

  • Admin App
    • New Added UI option to create a new study with duplicated sample IDs
    • Fixed Fix issue with opening of the app
    • Fixed Fix issue with disappearing default settings, when switching from DiaNN to Spectronaut and vice versa
  • New Comparison
    • Fixed Align PCA parameters for PX and PTM data to ProteomicsQC app
  • ScExplorer
    • Fixed Fixed issue with creation of pseudobulk studies
    • Fixed Fixed issue where operations in the study management panel did not work
    • Fixed Fixed issue with Celltypist prediction job on some instances
    • Fixed Fixed issue with the proper deletion of studies
  • Sample Selector (multiple apps)
    • New Automatically filter out any samples that are not fully integrated into PanHunter

PanHunter v22

General Apps

  • Admin App
    • Update Deactivate or Hide in UI the Pre-Processing on external instances
    • Update Allow update of sample table for integrated data without the need to re-process/re-integrate everything
    • Fixed Study deletion does not delete sample table xslx files in project folder
    • Fixed Sample table upload fails after successful validation
    • Fixed Sample table upload for Plate Seq asks for Sample ID
    • Fixed Project Leader who are NOT global admins are not able to add users to their project
    • Fixed Data service not enabled message appears before studies are shown
  • ScExplorer
    • New Add notification for the user about created gene set
    • New Add a placeholder text for empty gene set panel (private only)
    • New Send usage time statistics to Admin app
    • New Show the scExplorer logo as favicon
    • Update Improve IU of gene set tab panel
    • Update Enable closing of embedded selection with a click outside
    • Fixed Prevent histogram from covering annotation name
    • Fixed Wrong error message for duplicated gene set name creation
    • Fixed Form state is not preserved when switching embedding method bg job
    • Fixed 0 is missing for the legend within numerical shared annotations
    • Fixed Check uniqueness for all creation/renaming steps
    • Fixed Group all single values together and place them at the bottom of the annotations
    • Fixed Limit the resizing ability of the right side bar
    • Fixed Update the font in DE table and add hover behaviour to the rows
    • Fixed Incorrect warning displayed in Gene Sets tab
    • Fixed Embedding deletion does not update the state schema
    • Fixed Creating private numeric annotations from existing shared ones failed
  • ScDeepDive
    • Update Embeddings containing the string “pc” are removed
    • Fixed Pseudotime calculation fails for an embedding not containing all cells
    • Fixed User created embeddings/annotations are missing
  • Geneinfo
    • New Modify/Add option to get log transformed data
    • Fixed Fixed issue that led to crash in certain projects
  • GsetEnrVisualization
    • New Display loading animation until app is ready
    • Fixed GO:BP enrichment fails for single TopTable
  • New Comparisons
    • Update Remove conditional enabling of loading screen
    • Fixed Some successfully integrated studies were not displayed
    • Fixed Compare Comparisons tab showed error message after selecting a valid Comparison
    • Fixed Fixed issue with Analyze Categories in Exploratory Analysis (Sample Clustering Tab)
  • GeneComparison
    • New Display loading animation until app is ready
    • Fixed A false error was shown for some studies
  • MaPlot
    • New Display loading animation until app is ready
    • Fixed Start calculation only after both comparisons were selected
    • Fixed Fixed issue that led to a crash during startup
    • Fixed Fixed issue that lead to a creash for best match algorithm
    • Fixed Fixed issue with Feature table occupying too much space.
  • ProteomicsQC
    • New Display loading animation until app is ready
    • Fixed Fix issue with sample selector becoming unresponsive during start-up
  • TopTables
    • New Display loading animation until app is ready
    • Fixed Fixed issue where feature filters did not work properly when less than 4 Comparisons were selected
    • Fixed Enabled missing Compound activity estimation
  • PatientStats
    • New Display loading animation until app is ready
  • TrendAnalysis
    • New Display loading animation until app is ready
  • TFtargets
    • New Display loading animation until app is ready
    • Fixed Prevent app crash if TFTargets enrichment is missing for Comparison
  • Signatures
    • New Display loading animation until app is ready
  • Pathview
    • New Display loading animation until app is ready
  • NetworkVisualization
    • New Display loading animation until app is ready
  • Clustr
    • New Display loading animation until app is ready
  • SampleQC
    • New Display loading animation until app is ready

PanHunter v21

General Apps

  • Admin App
    • New Allow users to define a different set of parameters for proteomics data preprocessing
    • New Allow evaluation of results in ProteomicsQC of a specific proteomics preprocessing run before integrating results into PanHunter
    • New Deleting a study via the data management tab
    • New Allow users with role data manager or project lead to download public RNA-Seq data with GSE accession number via data management tab
    • Update Display error messages for failed preprocessing jobs
    • Update Minor app updates and refactoring
    • Fixed Study view is displayed again for eligible users
    • Fixed Improved validation of sample table during upload
  • Comparisons
    • New New button in Selected Samples tab to load alignment parameters on demand
  • MaPlot
    • Fixed Disable Detailed Plot in case the selected comparison does not contain the required data
    • Fixed Improved handling of big comparisons
  • PatientStats
    • Fixed Prevent app crash due to missing data
  • ProteomicsQC
    • New Added Sidebar Selector for selecting Preprocessing results that were created with the Admin App
    • Update Minor app updates and refactoring
  • GeneInfo
    • Fixed Changed text color for previously white-on-white text
  • ScExplorer
    • New It is now possible to resize the graph content
    • New Show error message if study registration failed
    • Update Moved graph annotations widgets into a new tab in the right sidebar
    • Update Harmonize categorical/numerical annotation display
    • Update Minor app updates and refactoring
  • Start Page
    • Update Removed redundant Tutorial button

PanHunter v20

General Apps

  • ProteomicsQC
    • Fixed Fixed the ability to select more than 1 study
    • Fixed Fixed that transformation dropdowns ignore the selected Study after application reset
  • ScExplorer
    • New Minor app updates and refactoring
    • New Added a new study selection panel
    • New Created the tools panel with 4 buttons for Dimension reduction, Clustering, DEG, psbulk
    • New Added radio button and checkboxes components to the right panel
  • New Comparison
    • New Minor app updates and refactoring
    • Fixed Resolved a bug where scExplorer was not starting
  • SampleQC
    • New Minor app updates and refactoring
  • ScDeepDive
    • New Minor app updates and refactoring
  • Enrichment Visualization
    • Fixed Comparison name showed in title of the individual comparisons tables
  • TopTables
    • New Minor app updates and refactoring
  • ProjectOverview
    • New Minor app updates and refactoring
  • MaPlot
    • New Minor app updates and refactoring
  • TFtargets
    • New Minor app updates and refactoring

PanHunter v19

General Apps

  • TopTables
    • Update Made user messages for Comparison Update more meaningful
    • Fixed Fixed multiple bugs in “Check Comparison” functionality
  • TFtargets
    • New Minor app updates and refactoring
  • ScExplorer
    • Update Allow creation of float-typed annotations
    • Fixed Resolved a bug where scExplorer was not starting
  • Enrichment Visualization
    • New Minor app updates and refactoring
  • Network Visualization
    • New Minor app updates and refactoring
    • Fixed Fixed ordering by top features
  • Signatures Visualization
    • New Minor app updates and refactoring
  • New Comparison
    • Update Enabled “delete embedding” button for unnamed embeddings
    • Fixed Fixed problem with random reshuffling
  • ProteomicsQC
    • New Now showing informative error message in place of Sample Selector
    • Update Improved label in Dimension Reduction plot (Sample Similarity tab)
    • Fixed Fixed issue with radio button reset after clear-all-button use
    • Fixed Restore default loading of preprocessing table columns
  • MaPlot
    • New UX app update and refactoring
    • New Now showing informative error message in place of Sample Selector
    • Update Improved label in Dimension Reduction plot (Sample Similarity tab)
    • Fixed Fixed FeatureID column
  • ScDeepDiven
    • Fixed Fixed issue with Pseudotime lineage saving fails
    • Fixed Fixed filtering of clusters with one cell for pseudotime
  • Gene Comparison
    • New Minor app updates and refactoring
  • Pathway Mapping
    • New Minor app updates and refactoring

Reference and meta data

  • Update Set uniform Roxygen version for CellTypes, Skeleton, GOenrichment, Base, Plotwrapr, GO, OmicsAgnostic, Msigdb, Plus, D3GeneTable and update documentation

PanHunter v18

General Apps

  • Start Page
    • New Projects now ordered alphabetically
    • New Added screen for projects under maintenance
    • Update Changed tab title from Admin to Start Page
    • Fixed The “Start Tour” button does not overlap start page notifications anymore
  • ProteomicsQC
    • New Added feature that allows to combine the Preprocessing QC parameters from multiple studies
    • Update Improved label in Dimension Reduction plot (Sample Similarity tab)
    • Fixed Fixed snapshot modal window
  • SampleQC
    • New Added Guided Onboarding Tour
    • Fixed App now prevents user from using too many samples to avoid crashes
  • ScExplorer
    • New The app now shows slide images for spatial studies
    • New Added Comparison naming
    • New Users now can delete Comparison tables they have created
    • New Implemented background job for pseudotime annotation
    • Fixed Fixed boundaries verification for the number of selected cells
    • Fixed Fixed Differential Expression job cancelling
  • ScDeepDive
    • New Minor app updates and refactoring
  • Patient Data
    • New Integrated “Subject Selector” in the app
    • Update Made Proportion checkbox available to more first variable types
    • Update Legend values now show feature name when OmicsFeature is selected
    • Update Added alternative visualizations in the Graphics tab
    • Fixed Fixed Genotyping data plots in Graphics tab
  • New Comparison
    • New Added Guided Onboarding Tour
    • Update Added file validity check before showing notification about saving a comparison
    • Update Deprecated usage of project pcutoff for comparisons calculation
    • Fixed Fixed notification about saving a comparison
  • Top Tables
    • New Added Guided Onboarding Tour
    • Update Added Top Features to the GO table
    • Fixed Fixed an issue that caused ‘Go To’ buttons to work only once
    • Fixed Fixed an issue that crashed the app when Max Features set to 0
  • MA Plot
    • Update Refactored feature to symbol mapping
    • Update Replaced Expression with Abundance
    • Fixed Fixed Comparison Group abundance type
    • Fixed App now handles the case when there are no significant features
  • Gene Info
    • New The app got a new style and improved user experience
  • Gene Clustering
    • New Added Guided Onboarding Tour
  • Signatures Visualization
    • New Added Guided Onboarding Tour
  • Enrichment Visualization
    • New Added Guided Onboarding Tour
  • TfTargets
    • New Added Guided Onboarding Tour
  • Admin App
    • New Added Confirmation window before deleting studies
    • Update “Data” tab now only visible for data managers and project leaders
    • Fixed Removed a hyperlink to the old start page in the header
  • Proteomics Preprocessing
  • New PGP can be run via snakemake on green product instances for the DiaNN PX pipeline

PanHunter v17

General Apps

  • Start Page
    • New Added Start Page Guided Onboarding Tutorial
    • New Added display of PanHunter version
    • Update “Reset Settings” button is now hidden for ScExplorer app
    • Fixed Fixed Start Page for users without project roles
  • ProteomicsQC
    • Fixed Fixed an issue with Export button being visible prior to study selection
    • Fixed Fixed a problem that caused app crash when Injection Order and/or Number of precursors is missing
    • Fixed Fixed subtitle in the Dimension Reduction plot
    • Fixed Fixed wrong label in the Dimension Reduction plot
    • New User selections stay selected when closing the tab
    • Fixed Snapshot links can be created now
    • Fixed User settings reset works also from the new start page
  • SampleQC
    • Update Mitochondrial plot improvements
  • ScExplorer
    • New App now gets studies list from Data Layer instead of environment variables
    • New App now displays the additional values from the Differential Expression analysis
    • New App now uses Data Layer as default annotation provider
    • New App now uses Data Layer for gene sets
    • New Added endpoint for retrieval of Differential Expression results
    • New Enabled deletion of shared gene sets
    • Update Memory usage improvements
    • Update Now updates study selection dropdown dynamically
    • Update Enable gene list storage via Data Service API
    • Update PCA key dropdown is now hidden when recalculate PCA is selected
    • Update Increased amount of top genes to 15
    • Fixed Renamed ‘category’ to ‘annotation’ where applicable
    • Fixed Fixed an issue where one corrupted study in the Data Layer prevents other studies to be registered
  • ScDeepDive
    • Fixed Fixed an issue that caused Pseudotime Calculation to fail
    • Fixed Fixed an issue that caused Cluster Comparison to fail
  • Project Overview
    • Update Allowed overwriting of already existing files
  • New Comparison
    • New Refactored visibility of control elements in some control panels
    • New Custom annotations are now displayed in the new comparison sample table
    • Update When Comparison Groups is updated, calculation parameters now saved in the new storage
    • Update Now Calculate button only shown after nominator and denominator are provided
    • Update Comparison recalculation will not be triggered anymore when user switches studies in new comparison tab
    • Update Wrapping of long annotation key values is now enforced to avoid style breaks
    • Update Made labels more omics agnostic
    • Fixed Fixed error message that was displayed after deselecting a study
    • Fixed Fixed an issue that caused new comparison to not be saved even if banner claims that table was saved
    • Fixed Annotation Keys starting with a digit were prefixed with X, now such keys are not valid
    • Fixed Fixed word-break behaviour in alerts
  • Top Tables
    • New Added standard error to Single Comparisons View tab
    • New Enabled loading of activity data from new storage
    • Update Improved shown columns in tables
    • Update ‘Table View’ improvements
    • Fixed Table for “Compound activity estimation” is not shown in new storage
    • Fixed Fixed Comparison Group overview table
    • Fixed Fixed an issue that caused Top Tables app to crash when changing Comparison Groups of different studies
    • Fixed Fixed link to the documentation page
    • Fixed Fixed column filtering for Comparison Groups overview
    • Fixed Fixed an issue that caused Comparison Overview table to show full timestamp when Comparisons are stored in data layer
  • MA Plot
    • New Added None option to plots tab
    • Update Updated comparison loading
    • Fixed Detailed plot displays abundance correctly for different omics types
  • Gene Info
    • Update Sample Selector is now always expanded on startup
  • Gene Comparison
    • Update Updated comparison loading
    • Update Made App compatible with feature list storage in data layer
  • Cross Comparison
    • Fixed Fixed plotting error that occured in the “Analyse few Match-Keys” tab
  • Pathway Mapping
    • Update Updated comparison loading
    • Update Added check for node label when highlighting genes with manual freetext feature input
    • Fixed Fixed an issue that caused app to crash when joining pathway nodes with feature metadata
    • Fixed Fixed link creation for tooltips of multi-coloured features in graph
    • Fixed Fixed an issue with finding the element clicked by the user
  • Network Visualization
    • Fixed Fixed input fillings from hyperlinks to the app
  • Enrichment Visualization
    • New Enrichment analysis now works with only up- or only down-regulated features too
    • New Enabled loading of activity data from new storage
    • Update Made warning messages for input ranges more verbose
  • Admin App
    • New Store species config data in project metadata field when creating projects
    • Update Project metrics block now shows “Data not available” instead of “0” when there’s no data
    • Fixed Added silent loading to background study info refresh
    • Fixed Fixed Project Deletion to avoid errors in Admin app
    • Fixed Fixed an issue that caused project policy upload to fail if there is no project directory

Other changes

  • Update Made busy indicator shown immediately on startup
  • Update Improved Data Layer performance
  • Update Multiple improvements in Sample Selector

Reference and meta data

  • Update Updated Wikipathways, MSigDB, Metabolon, ChipAtlas, BioGrid, GO and additional annotations

PanHunter v15

General Apps

  • The New Start Page
    • New The start page got a redesigned clean look with vertical apps lists and is now much faster
  • ProteomicsQC
    • Update Disabled right mouse button dragging on plotly plots
    • Fixed Fixed tooltip on the Quantifications - “How many features” plot
    • Fixed Fixed calculation of the Dimensionality Reduction Plot
    • Fixed Fixed Select Contaminants dropdown for the Quantity ranking plot
    • Fixed Fixed missing “None” in the Split by and Color by options
  • ScExplorer
    • New Added study management
    • New App now shows PanHunter loading page instead of default
    • New Added refresh button for study list
    • Update Changed intervals of page refresh and loading messages
    • Update App now updates the model list after a new model is created
    • Update App now relogins user if the old session has expired
    • Update App now prevents user from creating or renaming an embedding with an existing name
    • Update Welcome study replaced with a study selection page
    • Fixed Replaced outdated annotation names
    • Fixed Avoided redirects in API using trailing “/”
    • Fixed Fixed study registration
    • Fixed Fixed bug when no lasso selection is made
    • Fixed Fixed warnings in Louvain and Leiden jobs
  • ScDeepDive
    • Fixed Fixed a problem that caused the pseudo-time calculation to fail
  • New Comparison
    • New Selected Samples and Check Outliers tabs now validate the Sample Selection
    • Update Feature filtering options adapted for proteomics
    • Update The app displays the internal_ID instead of the feature ID for PTM
    • Fixed Fixed a problem with PTM comparisons that caused MA Plot app to crash
    • Fixed Fixed typos in help messages
  • Top Tables
    • New Split all links into Data and Go To panels
    • New Added function to export Comparison to CSVs
    • New App now shows “Show Comparison” and “Sample Table” buttons when using Comparison Data storage
    • New Implemented “Update” function for Comparison Data storage
    • New Implemented ‘Remove’ function for Comparison Data storage
    • New Added documentation about downloaded files from the app
    • Update More updates to support Comparison Data Storage
    • Update Improved and Extended the download of the Comparison zip
    • Update Cleaned-up Comparison overview table and added use of auto-generated names
    • Fixed Fixed empty UserID column in the comparison overview
    • Fixed Fixed a problem when the Comparisons Overview table remained empty after removing filters
    • Fixed Fixed Go To section links
    • Fixed Fixed handling of Comparison groups absence
  • MA Plot
    • New Detailed plot’s x-axis is fixed now, showing all contrast factor levels in any case
    • New Imputed values are now also displayed in the Detailed Plot tab
    • Update The app displays the internal ID instead of the feature ID for PTM
  • Pathway Mapping
    • New Implemented exact match for PTM/PTM and PTM/PG
    • Update The graph’s zooming was disabled till the app’s redesign
  • Network Visualization
    • Update Updates to support Comparison Data Storage
  • Signature Visualization
    • Update Updates to support Comparison Data Storage
    • Fixed Disabled right mouse button dragging on the plot
    • Fixed Fixed a problem that crashed app if no signature zscore data available
  • Enrichment Visualization
    • New Comparison Group data is loading from Data Layer in the migrated projects
    • Update PNG downloads were removed
    • Update Comparison Group tab was refactored to avoid lags and glitches
    • Fixed Fixed an issue that caused the “Comparison Groups” tab crash, if group has only one comparison
  • Admin App
    • New DataManagement: Implemented UI scaffolding for single-study view

Reference and meta data

  • Update PanHunter now uses the newest Ensembl version (111)
  • Update Removed mappings that do not match the EnsemblID pattern
  • Update Removed hamster annotations

PanHunter v14

General Apps

  • SampleQC
    • New New color scheme applied
  • ProteomicsQC
    • Update Added a warning message on plots if there are too many values for coloring and/or splitting
    • Update Added a warning message on Coefficient of Variation plot if CV cannot be computed
    • Update Improved explanations of the preprocessing tab
    • Fixed Fixed a problem with Dimensionality Reduction plot being pre-computed at startup
    • Fixed Fixed a problem with contaminants rank plot when sample table contains the column name “ID”
    • Fixed Fixed Feature Counts plot’s ordering
  • New Comparison
    • New New color scheme applied
    • Fixed Disabled TF targets analysis for peptidomics data
    • Fixed Suppressed Comparison data double saving
  • Top Tables
    • Fixed Fixed an issue that caused app’s crash for explosion of two PTM comparisons
    • Fixed Added a fix that prevents app from crashing if the projects does not contain any comparison groups
  • MA Plot
    • New New color scheme applied
    • New Added option to display Features names as labels on plots
    • New Detailed Plot can be colored based on metadata now
    • Update For peptidomics data the “Features to Highligh” will display internal ID instead of feature ID
    • Fixed Fixed an issue that caused missing features in multimappers
    • Fixed Fixed an issue that caused problems with plots zooming
    • Fixed Removed unrequired hovering value from the detail plot
  • Gene Info
    • New New color scheme applied
    • Fixed Fixed a problem that caused Zoom Plot to duplicate the default Plot
  • Gene Comparison
    • New New color scheme applied
  • Gene Clustering
    • New New color scheme applied
  • Pathway Mapping
    • New New color scheme applied
    • New The Pathway’s image is now zoomable
    • Update The app now uses internal PTM id instead of mapped feature id for PTM studies
    • Fixed Fixed an error that caused multiplied entries of the PTMs per gene symbol to be displayed
  • Network Visualization
    • New New color scheme applied
  • Signature Visualization
    • Update The message about the app not being designed for PTM studies added
  • Enrichment Visualization
    • New New color scheme applied
    • New Comparison Group tab now also uses ComparisonSelector with multi-selector capability
  • Admin App
    • New Added “About” block with the current PH version and useful links
    • Fixed Users: Fixed an issue that blocked removed users from being added again
    • Fixed Data Upload Wizard: Sample Table validation was failing for empty projects. Not a case anymore
    • Fixed Projects: Fixed an issue that blocked project updates from being saved due to the GitLab URL field
    • Fixed Contact Form: Fixed the issue when the form was not prefilled with project/app data in some cases
    • Fixed Fixed an issue that caused newly created project status be active instead of maintenance

Other changes

  • New The EvoSampleSelector now avoids empty and not meaningful columns
  • New “Clear The Filters” button was added in the EvoSampleSelector
  • New Comparison inputs now displays a short name instead of an ID
  • New All existing nameless comparisons now have a generated name
  • New The new knowledge center is used as the core of help documentation across PanHunter
  • Update The EvoTable’s “Select All” button now only select currently filtered elements
  • Update PanHunter internal links creation performance improvements

PanHunter v13

General Apps

  • SampleQC
    • Fixed Fixed an issue that caused app to crash when no QC data is available
    • Fixed Fixed an issue when selecting SUM as function on Samples/Conditions groups leads to a wrong column name
  • ProteomicsQC
    • New New control added to switch between density and counts for the distribution histogram plot
    • Update The amount of values by which the plot can be split is now limited
    • Update Changed default annotations within the quantification tab
    • Fixed Fixed “Contact Us” link
    • Fixed Fixed not user friendly errors in the quantification tab
    • Fixed Fixed broken “Clear all” button on the “Dimensionality Reduction” plot
    • Fixed Header Appearance Enhancements
    • Fixed Fixed situations when 1 dot on plots was not colored properly
  • New Comparison
    • Fixed Fixed an issue when sample annotations panel showed “Please enrich…” message even if already enriched
    • Fixed Fixed Exploratory analysis functionality for recently updated projects
  • Top Tables
    • New The app now uses a new Comparison Selector
    • Update Top tables were renamed to Comparisons across PanHunter
    • Fixed Fixed an issue that caused heatmap being showed/downloaded even if cancelled by user
    • Fixed Fixed an issue that caused pathway names being “NA” for up regulated features
  • MA Plot
    • New The app now uses a new Comparison Selector
    • New Added new UI elements to pick symbol and color variables for Volcano Plots
    • New Added input to allow user to select protein of interest
  • Gene Comparison
    • New The app now uses a new Comparison Selector
    • Fixed Fixed enrichment for PTM
  • Pathway Mapping
    • New The app now uses a new Comparison Selector
  • Network Visualization
    • New The app now uses a new Comparison Selector
  • Signature Visualization
    • New The app now uses a new Comparison Selector
  • Enrichment Visualization
    • New The app now uses a new Comparison Selector
    • Update Manual input fields harmonized
    • Fixed Fixed enrichment for PTM
    • Fixed Fixed preselection of comparisons via URL
  • Admin App
    • Notifications
      • New Notifications migrated from the Project Overview app to the Admin app. Allows project leaders to send notifications to users
    • Users
      • Fixed Fixed an issue where being on a non-first page in a user search causes missing results
      • Fixed Fixed an issue with server error if the same user was added to a project twice
    • Existing Projects
      • Fixed Fixed an issue that caused server error for projects with unknown status

Other changes

  • New Preprocessing adjusted to include microbial genome
  • New User guides for admin app added to the new Knowledge Center
  • New A new discard button added to ComparisonSelector
  • Update EvoSampleSelector is now automatically scaled to fit browser window size
  • Update Validate sample table adapted for bacteria
  • Update Login form changed to adapt fields to screen size
  • Fixed The “Awaiting Data” stub was removed from empty EvoTable

Reference and meta data

  • Update New reference genomes for H. sapiens, M. musculus and R. novegicus were installed. Now, both Ensemble Releases 110 and 111 are available.
  • Update The rat genome was improved most significantly in this release since the transition to the reference genome mRatBN7.2 was made compared to version 104. There are for example almost 5000 more protein-coding genes for rat in release 110 than in 104.

PanHunter v12

General Apps

  • Start Page
    • New The loading screen was updated to align the new PH theme
    • New Now app reads user’s permissions from the token instead of Redis
  • ProteomicsQC
    • New Feature Counts plot can now be split on subplots and/or sorted by selected value
    • New Feature Counts plot can now be sorted by selected value
    • New ‘Color by value’ option now added to plots:
      • Features with CV % variation
      • Coefficient of variation
      • Intensity distribution
    • New Contaminants tabs now disabled for peptidomics platforms
    • New Sample Selector harmonized across tabs
    • New Added Calculate and Clear all buttons to the ‘Precursors identified by injection order’ plot
    • Update All labels of the plots were generalize to adapt for each kind of data
    • Update ValidateSampleTable adapted also for peptidomics
    • Fixed Fixed an issue that prevent user from splitting and coloring plot by the same value
    • Fixed Fixed the problem with labels being not correct when bars are ordered by values
    • Fixed No more NA! Labels in the PCA plot for peptidomics are now displayed correctly
    • Fixed Fixed a problem with invisible white dots on plots
    • Fixed Fixed problems with Normalization dropdown in Intensities tab
  • Project Overview
    • Update Temporarily removed the ability to send messages to users - the feature will be redesigned
  • New Comparison
    • New The name for Top Tables can now be customized
    • New Top Tables overview table now also shows custom names
    • Update Added a warning if user tries to use excluded samples
    • Update Now only the applicable sections are shown in the left panel of the application
    • Fixed Fixed a problem that caused sample table in “Selected Samples” tab to shows only subset of annotations
    • Fixed Delete and Duplicate buttons are displayed in Sample Annotations panel
  • Top tables
    • New The sidepanel and header were redesigned, enhancing usability and appearance of the app
      • All UI elements and filters were rearranged and updated as well
    • New The application can now process Post-Translational Modifications data
    • New The app no longer triggers time-consuming recomputations when not necessary
    • New The all/most-recent top tables selection is now displayed only where it’s actually useful
    • New Each link to analyzes now have a useful description
    • Fixed Fixed an issue that prevented the top table from being selected with a first click
  • MA PLot
    • New The application can now process Post-Translational Modifications data
    • New A new “Detail plot” tab with a volcano plot implemented for PTM studies
  • ScBrowser
    • New PCA figure legends can now be divided into columns if they do not fit in the Plot area
    • New In addition, we now display up to 200 legends, instead of 50
  • Gene Info
    • New The application can now process Post-Translational Modifications data
    • Update Temporarily deactivated the “Reference Data” and “Find Genes” tabs
  • Gene Comparison
    • New PCA figure legends can now be divided into columns if they do not fit in the Plot area
    • Update The application can now process Post-translational modifications data
    • Update Alignment - Top Table selection dropdown list replaced with Top Table Selector
    • Update PCA tab was deactivated to avoid distinction with the New Comparison app
    • Fixed Heatmap coloring updated to bring more clarity to specific coloring combinations
  • Gene Clustering
    • New The application can now process Post-Translational Modifications data
    • Update Now only the applicable sections are shown in the left panel of the application
    • Update App output now saved as feature list, not top table
  • Pathway Mapping
    • New The sidepanel was redesigned, enhancing usability and appearance of the app
    • New UI elements were rearranged and tooltips updated to improve UX
    • New The application can now process Post-Translational Modifications data
  • Network Visualization
    • New The application can now process Post-Translational Modifications data
    • Fixed Fixed an issue with floating genes that are not connected to anything
    • Fixed Fixed an issue where species could not be changed using the Network Species option
  • Signature Visualization
    • Fixed Fixed link issue in the app’s documentation
  • Enrichment Visualization
    • New App can now perform enrichment analysis for Post-Translational Modifications data
  • Admin App
    • Activities
      • Fixed Fixed an issue with checkbox status change breaking pagination
  • Users
    • New Added support to filter users not only by emails, but also by registration date and role
  • Existing Projects
    • New Now users can see exactly what role they have in the project
    • New Users can now create, manage and add project-specific apps using UI
    • Non-admin data manager can now view a list of users
    • Fixed Fixed an issue where project managers who are not administrators could not edit the Information tab
  • Admin App
    • Data Upload Wizard
      • New Communication emails on sample table upload now sent to Project Leaders and Data Managers of the project
      • Fixed Fixed an issue when sample table was not uploaded

Other changes

  • New EvoReport now uses data.tree to represent content structure and other improvements
  • Update The Pfam website was decommissioned, so we have updated all links to entries
  • Update Same with the National Library of Medicine website and CAS numbers
  • Update Scatter plots can now use non-numeric values on x-axis
  • Fixed Column filters can now work with logical columns

PanHunter v10

General Apps

  • ProteomicsQC
    • New Added “Calculation in Progress” notification
    • New Added Spectronaut parser as an additional entry point
    • Update Error messages are more user-friendly now
    • Update Updated the cumulative plot in the quantification tab
    • Update Replaced all bar and box plot occurrences with plotwrapr
    • Fixed Now all drop-downs behave properly when their value is empty
    • Fixed Added handling for situations when coloring and splitting options are identical
    • Fixed Fixed an issue with Injection Order plot disappearing after changes in the sample selector
    • Fixed Clear All button in Sample Similarity tab does not produce error anymore
  • Start Page
    • New Project specific apps added to the start page
  • Project Overview
    • Fixed Fixed issue with dashboard barplot: X-axis labels were cutoff and overlaying with axis title
  • Signature Visualization
    • New The app now uses TopTableSelector instead of drop-down
    • Update Now shows harmonized top table labels
  • Top tables
    • New On the “Compare Top Tables tab” all drop-downs were replaced with TopTableSelector
    • Update Now shows harmonized top table labels
    • Update Allowed loading of comparison groups with missing comparisons
    • Fixed Fixed download of top tables
    • Fixed Fixed loading of the missing comparison in Comparison Groups tab
  • MA PLot
    • Update Now shows harmonized top table labels
  • Gene Clustering
    • Update Now shows harmonized top table labels
  • Pathway Mapping
    • Update Now shows harmonized top table labels
    • Fixed Removed escape and new-line symbols from descriptions
  • Network Visualization
    • Update Now shows harmonized top table labels
    • Fixed Fixed app crash when changing network species to HS
    • Fixed Fixed subsetting of vector with list
  • New Comparison
    • New New custom annotations are directly visible in the sample selector on fly
  • Admin App
    • Activities
      • Fixed Fixed an issue when switching between projects would cause an error
    • Users
      • Fixed Fixed an issue when project roles for logged in user are not kept in sync
    • Project Creation
      • New A new switch allows to instantly include Patient Data in a new project
      • Fixed Validation messages now disappear after entering a valid input
      • Fixed No need to update the page - newly created project are now editable immediately
    • Existing Projects
      • New Project leaders can now delete empty projects via UI
      • Update User access to the project now checked when project URL manually entered in the address bar
      • Fixed Fixed an issue with project user listing only worked for global admins
      • Fixed Fixed an issue when non-admin project leaders could not add users to a project
      • Fixed Fixed an issue when project leaders list showed wrong first and last names
    • Data Upload Wizard
      • Update The file upload logic in Data Upload Wizard has been improved
      • Fixed Job status timestamp is now more user friendly
    • Contact Form
      • Fixed Fixed an issue with empty contact form when redirected from application

Other changes

  • New Reactive context added to the Top Table Selector
  • Update EvoData extended to make it suitable for storing TT and CGs
  • Fixed Fixed an issue when starting TT calculation with two users at the same time can bring down external instances