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Commits on Nov 25, 2022

• Input and plot update

  

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Commits on Nov 28, 2022

• Solved golem::run_dev bug. Updated namespaces.

  

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• Merge pull request ndcn#15 from dolivierj/dev

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Commits on Dec 1, 2022

• Added Unsaturation plot.

  

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Commits on Dec 5, 2022

• Added basic PCA

  

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Commits on Dec 8, 2022

• Changed colorset, updated PCA

  

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• Merge pull request ndcn#16 from dolivierj/dev

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• Added Damien as author.

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• Added bioconductor as repository to install packages from.

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• Fix build errors

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• Added ORCID id of Damien.

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• Merge pull request ndcn#19 from ricoderks/dev

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• Fixed recalculation to the initial comparisson of the volcano plot after changing the comparisson.

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• Merge pull request ndcn#20 from ricoderks/dev

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Commits on Dec 12, 2022

• Added basic login

  

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• Merge pull request ndcn#23 from dolivierj/dev

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• bump version

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• Tried to fix warning in build check.

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• Merge pull request ndcn#25 from ricoderks/dev

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• attempt 2

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• bump version

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• attemp 3

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• attempt 4

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• Merge pull request ndcn#26 from ricoderks/dev

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Commits on Jan 11, 2023

• Initial commit for moded SODA

  

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• Resetting SODA after deleting old version

  

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• Testing bugs on plot displays

  

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Commits on Jan 12, 2023

• Added more visual feedback on lipid classes and feature count during lipids upload. Corrected unique ID feedback on lipids upload. Changed spacing for feature and sample filter in lipids filtering.

  

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• Finished plot preview of classes during feature filtering. Added most of the UI for sample filtering, but not yet functionnal.

  

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Commits on Jan 13, 2023

• Filtering in upload lipids conceptually finished (for the main parts of it). Organising the script will be necessary.

  

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Commits on Jan 16, 2023

• Save before shinydashboard -> bs4dash conversion

  

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• Switched from shinydashboard to bs4dash to debug bs4dash boxes.

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• Corrected self$get_idx_samples

  

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• Solved blank multiplier bug (unresponsive)

  

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• Solved feature filter bug when thresholds are 0.

  

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• Added feature filtering interactivity as soon as lipids data is uploaded

  

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Commits on Jan 17, 2023

• Finished lipids upload module. Changed widgets to fill space.

  

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Commits on Jan 18, 2023

• Horrible spawn plotboxes prototype in visualise lipids.

  

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Commits on Jan 19, 2023

• plotting nightmare part 2

  

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Commits on Jan 20, 2023

• Plotboxes update : functionnal again but rolledback to unoptimised spawn plot every time a box is called.

  

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• Added hardcoded volcano plot (needs sidebar to interactively select metadata groups)

  

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Commits on Jan 23, 2023

• Added sidebars to plotboxes. Made them interactible with currently available plots (class comparison, class distribution, volcano plot)

  

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Commits on Jan 24, 2023

• Plots update : added PCA scores and loadings, added double bond plots (bugged for anything but genotype). Added a plotly hover to Class comparison plot.

  

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Commits on Jan 26, 2023

• Redesigning plotboxes. Updated class distribution, class comparison and volcano plot.

  

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Commits on Jan 27, 2023

• Plotboxes updated for all plots. Discarded interactive complex heatmaps as they do not work in shiny modules.

  

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• Finished migrating lipids visualisation to soda module version. Heatmap is now default plotly and must be improved.

  

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• Merge pull request ndcn#29 from dolivierj/dev_mod

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Commits on Jan 30, 2023

• Expanded the Help tab with comments about the data uploads and filtering. Improved the class preview plot with clearer background and numbers.

  

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• Merge pull request ndcn#37 from dolivierj/dev_mod

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• Improved documentation, debugged volcano plot, added exports to the volcano table and filtered data.

  

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• Merge pull request ndcn#40 from dolivierj/dev_mod

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• Added some additional download buttons for the produced data. Solved the normalise_class method bug when filtering out too much data.

  

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• Merge pull request ndcn#42 from dolivierj/dev_mod

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Commits on Jan 31, 2023

• Updated the heatmap with a percentile slider (work in progress). Increased max upload file sie from 5MB to 30MB.

  

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• Merge pull request ndcn#43 from dolivierj/dev_mod

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• Improved reactivity on row exclusion in the metadata filtering.

  

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• Merge pull request ndcn#44 from dolivierj/dev_mod

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Commits on Feb 1, 2023

• Added lipid filtering skip. Altered data handling to calculate p-values and fold changes.

  

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• Merge pull request ndcn#47 from dolivierj/dev_mod

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• Completed fold change and p-value imputation for groups containing only NAs.

  

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• Added more info on the volcano plot documentation.

  

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• Merge pull request ndcn#49 from dolivierj/dev_mod

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• Improved volcano table documentation.

  

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• Merge pull request ndcn#50 from dolivierj/dev_mod

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Commits on Feb 2, 2023

• Added interactive heatmap with heatmaply.

  

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• Version updated

  

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• Merge pull request ndcn#51 from dolivierj/dev_mod

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• Fixed color vector. Changed sample metadata filtering to also have keep rows in addition to drop rows.

  

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• Merge pull request ndcn#52 from dolivierj/dev_mod

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Commits on Feb 3, 2023

• Improved documentation. Omics_object class reorganised for tables and application adapted. Feature filter based on classes or manual selection begun, but conflicts in interaction with the blank and…

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• Merge pull request ndcn#53 from dolivierj/dev_mod

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Commits on Feb 6, 2023

• test_comit

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• Omics_data object reorganisation.

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• Merge pull request ndcn#56 from dolivierj/dev_mod

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• Aestherical update to the meta upload filtering

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• Fixed feature filter. Next : update the feature count progress bar.

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• Merge pull request ndcn#57 from dolivierj/dev_mod

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Commits on Feb 8, 2023

• Major updates. Indices in Omics_data improved. Metadata upload adapted, lipidomics data adapted, feature filter on lipid classes finished. Debugged filter filtering when going back and forth from r…

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• Merge pull request ndcn#58 from dolivierj/dev_mod

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• Updated test data.

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• Merge pull request ndcn#59 from dolivierj/dev_mod

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Commits on Feb 9, 2023

• Added authentification. Documentation in progress.

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• Merge pull request ndcn#60 from dolivierj/dev_mod

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• Version update.

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• Improved the help tab for data upload.

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• Merge pull request ndcn#61 from dolivierj/dev_mod

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Commits on Feb 10, 2023

• Download update. Added download options to all plot tables, except the class comparison.

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• Merge pull request ndcn#62 from dolivierj/dev_mod

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Commits on Feb 16, 2023

• Browse button set above the preview tables in the upload tabs. Major additions to documentation, work in progress.

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• woops

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• Merge pull request ndcn#67 from dolivierj/dev_mod

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• Solved persisting last plot in visualisation.

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• Merge pull request ndcn#68 from dolivierj/dev_mod

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Commits on Feb 17, 2023

• Basic visualisation documentation finished.

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• Merge pull request ndcn#70 from dolivierj/dev_mod

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• Basic table description added. Must be improved.

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Commits on Feb 22, 2023

• Performance update. Switched from dataframe to matrix where possible. Did not manage to make class comparison run faster because of how the interactivity must be done.

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• Merge pull request ndcn#71 from dolivierj/dev_mod

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Commits on Feb 27, 2023

• Feature filtering update

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• Merge pull request ndcn#78 from dolivierj/dev_mod

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Commits on Feb 28, 2023

• Double bonds plot update.

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• Merge pull request ndcn#80 from dolivierj/dev_mod

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• Table choice update.

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• Merge pull request ndcn#84 from dolivierj/dev_mod

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Commits on Mar 2, 2023

• Minor patches.

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• Merge pull request ndcn#86 from dolivierj/dev_mod

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• PCA patch

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• Merge pull request ndcn#87 from dolivierj/dev_mod

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Commits on Mar 7, 2023

• Update 0.2.20 - general

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• Merge pull request ndcn#88 from dolivierj/dev_mod

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Commits on Mar 8, 2023

• Patch 0.2.21 - Volcano plot

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• Merge pull request ndcn#89 from dolivierj/dev_mod

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• Update 0.2.22 - Volcano plot

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• Merge pull request ndcn#90 from dolivierj/dev_mod

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• Update 0.2.23 - Data upload

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• Merge pull request ndcn#91 from dolivierj/dev_mod

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• Update 0.2.24 - Missing values

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• Update 0.2.25 - download zip

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• Merge pull request ndcn#95 from dolivierj/dev_mod

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Commits on Mar 9, 2023

• Update 0.2.26

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Commits on Mar 13, 2023

• Update 0.2.27 - Table merger

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• Merge pull request ndcn#97 from dolivierj/dev_mod

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Commits on Mar 23, 2023

• Update 0.2.28 - Plotting preupdate

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• Merge pull request ndcn#99 from dolivierj/dev_mod

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Commits on Mar 28, 2023

• Update 0.3.0 - Persistency update

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• Merge pull request ndcn#100 from dolivierj/dev_mod

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Commits on Mar 29, 2023

• Update 0.3.01 - Prepropteomics patch.

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• Merge pull request ndcn#101 from dolivierj/dev_mod

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Commits on Mar 30, 2023

• Patch 0.3.02 - Proteomics upload

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• Merge pull request ndcn#102 from dolivierj/dev_mod

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Commits on Mar 31, 2023

• Patch 0.3.03 - Uniprot requests.

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• Merge pull request ndcn#103 from dolivierj/dev_mod

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• Patch 0.3.04 - Proteomics upload

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Commits on Apr 3, 2023

• Patch 0.3.05 - Volcano table bug

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• Merge pull request ndcn#104 from dolivierj/dev_mod

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Commits on Apr 4, 2023

• Patch 0.3.06 - minor improvements

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• Merge pull request ndcn#105 from dolivierj/dev_mod

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Commits on Apr 5, 2023

• Patch 0.3.07 - Proteomics plots

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• Merge pull request ndcn#106 from dolivierj/dev_mod

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• Patch 0.3.08 - T-test

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• Merge pull request ndcn#107 from dolivierj/dev_mod

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• Patch 0.3.09 - Debug

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• Patch 0.3.10 - Discriminant analysis

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• Patch 0.3.11 - Updates on proteomics.

  

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• Patch 0.3.14 - General updates.

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• Patch 0.3.15 - Blank filtering.

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• Patch 0.3.16 - NA imputation.

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• Patch 0.3.19 - color selection

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• Patch 0.3.20 - Color palette.

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• Patch 0.3.24 - GSEA

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• Patch 0.3.26 - Interactive GSEA

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• Patch 0.3.27 - GSEA reactivity improvement.

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• Patch 0.3.28 - CNET plot improvements.

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• Patch 0.3.29 - Transcriptomics

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• Patch 0.3.30 - T-test debug

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• Update 0.4.00 - Proteomics and transcriptomics.

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• Patch 0.4.01 - Gene names update

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• Patch 0.4.2 - Debugs

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• Patch 0.4.3 - Volcano plots

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• Patch 0.4.4 - Reactivity debug

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• Patch 0.4.5 - DA patch

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• Patch 0.4.6 - Debug and img formats.

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• Patch 0.4.7 - Routine

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• Bump version

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• Patch 0.5.1 - selection

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• Patch 0.5.2

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• Patch 0.5.3 - Clear plots debug

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• Patch 0.5.4 - Clear plots

  

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• Merge conflict solved.

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• Merge pull request ndcn#157 from ndcn/dev

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• Update DESCRIPTION

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• The raw table for download was not update when Blank & Group filtering settings where adjusted. This is fixed now.

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• Merge pull request ndcn#158 from ricoderks/issue_sascha

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Commits on Jan 12, 2024

• Merge branch 'dev' into dev

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• fixed merge conflict.

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• Remove login

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• Add some more informative error messages.

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• Fix problem when the a group column contains integers, mainly zero's gives a problem. Convert to character.

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• Bump version.

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• Fixed problem with total class normalization table in the volcano plot.

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• Bump version.

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• New fix to convert the whole meta data table to character.

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• Fixed issues with NA in the meta data.

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• Removed debug stuff.

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