What's Changed

• Dev card clipping (JS function) by @ivokwee in https://github.com/bigomics/omicsplayground/pull/606
• Fix #596: Add tooltips to the accept/cancel and resend/cancel in sharing tab by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/608
• Dev remote auth by @ivokwee in https://github.com/bigomics/omicsplayground/pull/610
• Message user when pgx compute process succeeds by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/612
• Warn user and CS user when pgx compute process fails by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/611
• feat: email user when pgx is completed by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/617
• add scale per method option, set default=TRUE by @phisanti in https://github.com/bigomics/omicsplayground/pull/616
• Fix #607 - gene methods and gene set methods fails when there is only one sample in a group by @ShaliniPandurangan in https://github.com/bigomics/omicsplayground/pull/615
• remove Keyword option under word cloud by @ShaliniPandurangan in https://github.com/bigomics/omicsplayground/pull/619
• Fix only one sample in all the groups by @ShaliniPandurangan in https://github.com/bigomics/omicsplayground/pull/625
• Notify logged in user when a new dataset is received by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/626
• Add multiple choices gene and geneset annotation by @ShaliniPandurangan in https://github.com/bigomics/omicsplayground/pull/629
• fix functional clusters annotation mismatch by @ShaliniPandurangan in https://github.com/bigomics/omicsplayground/pull/631
• Improve UI/UX of volcano plots by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/633
• fix userdir for dataset2 by @ivokwee in https://github.com/bigomics/omicsplayground/pull/635
• Dropdown moved to bslib popover by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/644
• Update README documentation by @phisanti in https://github.com/bigomics/omicsplayground/pull/648
• Fix #620: improve pgx computation spinner by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/645
• Interactive plot #472 by @phisanti in https://github.com/bigomics/omicsplayground/pull/647
• Disable browser back and forward buttons in firefox by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/653
• Fix #649: Enrichment analysis has first column truncated by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/654
• recode: give plot/table output unique name using ns() by @ivokwee in https://github.com/bigomics/omicsplayground/pull/655
• Fix #621: Add a separate column in tables that has link to genes/proteins by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/646
• Scm recompute feature by @phisanti in https://github.com/bigomics/omicsplayground/pull/660
• Testing of Omics Playground by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/650
• Fix reactivity in board.compare by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/663
• Fix heatmap not appearing (issue #662) by @ivokwee in https://github.com/bigomics/omicsplayground/pull/669
• Allow pgx to be saved locally via bash command by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/668
• Board testing by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/672
• Upload preview v2 by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/656
• Improve build of docker opg:base and opg:latest by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/678
• Fix #681: column type and name by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/682

Full Changelog: https://github.com/bigomics/omicsplayground/compare/v3.2.15...v3.2.26

What's Changed

• Bigui by @JohnCoene in https://github.com/bigomics/omicsplayground/pull/119
• Cicd by @marcosci in https://github.com/bigomics/omicsplayground/pull/121
• Revert "Cicd" by @ivokwee in https://github.com/bigomics/omicsplayground/pull/123
• Modals - remove shinyBS by @JohnCoene in https://github.com/bigomics/omicsplayground/pull/124
• Multi-package folder structure (components) by @ivokwee in https://github.com/bigomics/omicsplayground/pull/125
• Sass by @JohnCoene in https://github.com/bigomics/omicsplayground/pull/127
• Pgx as reactiveValue by @ivokwee in https://github.com/bigomics/omicsplayground/pull/128
• maximimizing plots in fullscreen zoom by @ivokwee in https://github.com/bigomics/omicsplayground/pull/138
• Revert "Pgx as reactiveValue" by @ivokwee in https://github.com/bigomics/omicsplayground/pull/139
• PGX object as reactiveValues by @ivokwee in https://github.com/bigomics/omicsplayground/pull/141
• Matt UI by @ivokwee in https://github.com/bigomics/omicsplayground/pull/146
• Update dataviz from develop by @z3tt in https://github.com/bigomics/omicsplayground/pull/145
• TimerModule & referrals by @ivokwee in https://github.com/bigomics/omicsplayground/pull/147
• UI by @JohnCoene in https://github.com/bigomics/omicsplayground/pull/159
• test pull request (example docstring) by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/169
• test branch by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/170
• moved static ui components in UploadModule out of server; removed som… by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/173
• board.biomarker -> plotModule refactor by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/174
• Convert drugconnectivity board to plotmodule by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/175
• Plotly styling by @z3tt in https://github.com/bigomics/omicsplayground/pull/172
• Develop expression plot module by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/176
• Develop plot module refactor by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/177
• Develop board functional refactor by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/178
• Develop board wordcloud refactor by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/179
• board.enrichment refactor by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/180
• board.tcga refactor by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/182
• board.signature refactor by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/181
• Develop board expression refactor by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/183
• Develop board.singlecell refactor by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/184
• Develop board.connectivity refactor by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/186
• board.wgcna refactor by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/187
• clean code - see description by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/185
• Boxplot conversion to plotly by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/188
• Fixes before release - xavier by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/189
• Develop plot reactivity fixes by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/191
• 'barplot' conversion to plottly by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/190
• Develop fix load dataset by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/193
• New TableModule by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/192
• "try example dataset" button loads the right dataset; modal if not found by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/194
• subplot barplot conversion to plotly by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/195
• Develop plot options by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/196
• Develop branch moves to master by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/197
• Dev org rat by @ivokwee in https://github.com/bigomics/omicsplayground/pull/200
• Edit data description by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/203
• Dev settings container by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/204
• Public datasets loading by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/205
• Input data pgx convert by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/223
• create Shiny wrappers around bigdash JS triggers... end of JS PITA.. by @ivokwee in https://github.com/bigomics/omicsplayground/pull/221
• fix: diffexpr plots blink and initialize to all genes selected by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/226
• replace ngs and inputData with pgx by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/228
• remove inputData and ngs refs in favor of pgx by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/227
• make separate shared tsne by @ivokwee in https://github.com/bigomics/omicsplayground/pull/240
• Share datasets by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/241
• Dev home by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/247
• Dev-cards-bs5 by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/250
• Revert "Dev-cards-bs5" by @ivokwee in https://github.com/bigomics/omicsplayground/pull/251
• fix: contrasts tab now has auto-suggestion and shows compute tab by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/252
• #249/gene table not reacting by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/254
• #246/parallel coordinates plot not appearing by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/255
• Plots inside cards by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/256
• Display shiny errors by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/259
• Update globally the copyright year by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/260
• files with no copyright fix by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/267
• Move to playbase by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/277
• Refactoring captions by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/278
• Background computation of pgx by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/274
• Refactoring captions by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/280
• Refactoring captions by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/281
• Cards header improvement by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/283
• feat: double plot download resolution by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/294
• fix issue #232 on OPG by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/290
• feat: new loading spinner by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/293
• Update README.rst by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/285
• Clustering features with phenotype selector by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/286
• Compute error by @ivokwee in https://github.com/bigomics/omicsplayground/pull/309
• Fix #272 pca/tsne 3D plot not working by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/305
• Revert "feat: double plot download resolution" by @ivokwee in https://github.com/bigomics/omicsplayground/pull/311
• Fix #304 - Social buttons do not work at time out modal by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/313
• Improve plots when datasets have large number of features and samples by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/306
• ivo changes by @ivokwee in https://github.com/bigomics/omicsplayground/pull/315
• fix: select correct rows by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/324
• fix sample information plotting options by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/325
• Dev margin plots by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/323
• Fix plot download by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/330
• Fix validate/error messages showing on card header by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/331
• Fix margins plots by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/332
• Dev wgcna by @ivokwee in https://github.com/bigomics/omicsplayground/pull/338
• #335: from tipify to withToolTip by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/339
• fix: #341 GTEX: No need to display HEX colour by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/344
• flush stderr/stdout from background processx to avoid blocking by @ivokwee in https://github.com/bigomics/omicsplayground/pull/345
• feat: add show_legend parameter by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/351
• launch individual boards really quickly by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/349
• convert resources tab tables to TableModule; remove tableModule file … by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/358
• Fix #314 Watermarking does not work anymore by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/357
• Added cards inside PlotModule by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/253
• fix: #354 Proportions plot bug in singlecell board by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/356
• remove a conditional panel from plotmodule by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/366
• Add sample filter to biomarker board by @ivokwee in https://github.com/bigomics/omicsplayground/pull/369

New Contributors

• @marcosci made their first contribution in https://github.com/bigomics/omicsplayground/pull/121
• @ncullen93 made their first contribution in https://github.com/bigomics/omicsplayground/pull/169
• @mauromiguelm made their first contribution in https://github.com/bigomics/omicsplayground/pull/176
• @ESCRI11 made their first contribution in https://github.com/bigomics/omicsplayground/pull/177

Full Changelog: https://github.com/bigomics/omicsplayground/compare/v2.8.18...v3.0-RC9

Last version of the old UI application (as of March 1, 2023). Now maintained via the "v2" branch.

New UI update

What's Changed

• Bigui by @JohnCoene in https://github.com/bigomics/omicsplayground/pull/119
• Cicd by @marcosci in https://github.com/bigomics/omicsplayground/pull/121
• Revert "Cicd" by @ivokwee in https://github.com/bigomics/omicsplayground/pull/123
• Modals - remove shinyBS by @JohnCoene in https://github.com/bigomics/omicsplayground/pull/124
• Multi-package folder structure (components) by @ivokwee in https://github.com/bigomics/omicsplayground/pull/125
• Sass by @JohnCoene in https://github.com/bigomics/omicsplayground/pull/127
• Pgx as reactiveValue by @ivokwee in https://github.com/bigomics/omicsplayground/pull/128
• maximimizing plots in fullscreen zoom by @ivokwee in https://github.com/bigomics/omicsplayground/pull/138
• Revert "Pgx as reactiveValue" by @ivokwee in https://github.com/bigomics/omicsplayground/pull/139
• PGX object as reactiveValues by @ivokwee in https://github.com/bigomics/omicsplayground/pull/141
• Matt UI by @ivokwee in https://github.com/bigomics/omicsplayground/pull/146
• Update dataviz from develop by @z3tt in https://github.com/bigomics/omicsplayground/pull/145
• TimerModule & referrals by @ivokwee in https://github.com/bigomics/omicsplayground/pull/147
• UI by @JohnCoene in https://github.com/bigomics/omicsplayground/pull/159
• test pull request (example docstring) by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/169
• test branch by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/170
• moved static ui components in UploadModule out of server; removed som… by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/173
• board.biomarker -> plotModule refactor by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/174
• Convert drugconnectivity board to plotmodule by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/175
• Plotly styling by @z3tt in https://github.com/bigomics/omicsplayground/pull/172
• Develop expression plot module by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/176
• Develop plot module refactor by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/177
• Develop board functional refactor by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/178
• Develop board wordcloud refactor by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/179
• board.enrichment refactor by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/180
• board.tcga refactor by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/182
• board.signature refactor by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/181
• Develop board expression refactor by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/183
• Develop board.singlecell refactor by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/184
• Develop board.connectivity refactor by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/186
• board.wgcna refactor by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/187
• clean code - see description by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/185
• Boxplot conversion to plotly by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/188
• Fixes before release - xavier by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/189
• Develop plot reactivity fixes by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/191
• 'barplot' conversion to plottly by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/190
• Develop fix load dataset by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/193
• New TableModule by @ESCRI11 in https://github.com/bigomics/omicsplayground/pull/192
• "try example dataset" button loads the right dataset; modal if not found by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/194
• subplot barplot conversion to plotly by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/195
• Develop plot options by @mauromiguelm in https://github.com/bigomics/omicsplayground/pull/196
• Develop branch moves to master by @ncullen93 in https://github.com/bigomics/omicsplayground/pull/197

New Contributors

• @marcosci made their first contribution in https://github.com/bigomics/omicsplayground/pull/121

Full Changelog: https://github.com/bigomics/omicsplayground/compare/v2.8.0...v3.0.0

Release Notes

Release update based on Ubuntu 20.04 LTS and R 3.6.3.

Requirements

• Ubuntu 20.04
• R 3.6.3
• Bioconductor 3.10

Matching docker release

• docker pull bigomics/omicsplayground:v2.4 .

Features

• New: correlation module, connectivity module
• Redesigned CellProfiing module
• New nested menu structure
• Better messaging
• PDF export also for plotly GL-based figures using orca

Release Notes

Second major release. The front-end Shiny code has been completely overhauled using pure R/Shiny (previously it was using Rmarkdown/Shiny) and using Shiny modules. Startup should be much improved now. Note the change in Ubuntu, R and Bioconductor versions. The nickname was chosen because using Shiny modules and pure R/Shiny is a 'better base' for future development.

Requirements

• Ubuntu 19.10
• R 3.6.1
• Bioconductor 3.10

Matching docker release

• docker pull bigomics/omicsplayground:v2.0 .

New Features

• Restructured ui/server code
• Faster startup time

Release Notes

First public release. This release was succesfully built on Ubuntu 19.04 with R 3.5.2 and Bioconductor 3.8. The matching docker release is bigomics/omicsplayground:v1.0 . This source code and docker release is compatible with the journal publication in NAR Genomics and Bioinformatics (see below). The nickname was chosen because we were 'always almost' ready to release.

Requirements

• Ubuntu 19.04
• R 3.5.2
• Bioconductor 3.8

Matching docker release

• docker pull bigomics/omicsplayground:v1.0 .

New Features

• Compatible with Omics Playground journal publication: Akhmedov M, Martinelli A, Geiger R and Kwee I. Omics Playground: A comprehensive self-service platform for visualization, analytics and exploration of Big Omics Data. NAR Genom Bioinform, Volume 2, Issue 1, March 2020, lqz019.