v3.2.26

What's Changed

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

Full Changelog: v3.2.15...v3.2.26

v3.0 Release candidate RC9

What's Changed

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

v3.0.0

New UI update

What's Changed

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

New Contributors

• @marcosci made their first contribution in #121

Full Changelog: v2.8.0...v3.0.0

v2.8.18

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

v2.4.1

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

v2.0 (better base)

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

v1.0 (always almost)

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.