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CHANGELOG.md

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v3.5.0 (2024-11-08)

  • new: mockup file menu view
  • merge master & resolve conflicts view
  • merge master & resolve conflicts view
  • first empty prototype view
  • feat: clear info symbols view
  • feat: clean info symbols view
  • activate outliers pannel; change default options to current default setting view
  • refactoring to simplify code; rename X to countsX view
  • minor fix for passing X from batch correction module to pgxcompute view
  • pass countsX to playbase pgx computation as X matrix (needs review) view
  • Update upload_module_preview_counts.R view
  • Update upload_module_preview_counts.R view
  • upload_module_outliers.R: added logMaxMedianNorm & logMaxSumNorm view
  • Update upload_module_outliers.R view
  • upload_module_outliers.R: renamed NNM to NPM view
  • upload_module_outliers.R: added las=1 in boxplots view
  • upload_module_outliers.R: added option 'skip imputation' view
  • upload_module_outliers.R: minor fix in skip imp view
  • Update upload_module_outliers.R view
  • upload_module_outliers.R: update skip_imput view
  • added las=1 to boxplots and hists view
  • added las=1 to boxplots and hists view
  • upload_module_outliers.R: added playbase::counts.mergeDuplicateFeatures taking into account presence/absence of NA values. view
  • upload_module_outliers.R: added las=1 in outlier detection plot view
  • upload_module_outliers.R: added las=1 in outlier detection PCA plot view
  • feat: disable qc/bc plot maximization view
  • add basic template for dataset report view
  • refactor and simplify server side; remove reactive return for module (not needed) view
  • upload_module_outliers.R: fix dim(counts) != dim(X) with playbase::counts.mergeDuplicateFeatures view
  • clean up, attempt to dbg why show_report_modal is not working view
  • fix namespace issue that did not allow event listener on button; improve button ui view
  • fix Argument 3 can't be empty; improve ui; add body content view
  • inject api url into shiny via .Renviron view
  • retrieve datasets with jwt authentication view
  • update datasets at every ui render (since datasets might change after session is initiated) view
  • add download handler for quarto report view
  • attempt to get pdf from quarto output to download handler view
  • fix download handler to return pdf file view
  • close modal; warn user that download is coming soon view
  • upload_module_outliers.R: added dbg("[outliers_server] Skip imputation") for monitoring view
  • upload_module_outliers.R: added comment for imputedX. Removed pmax(log2(2**X)) view
  • upload_module_computepgx.R: added checks dim(params$counts) & dim(params$countsX) view
  • upload_module_outliers.R: added dim check for correctedX before return() view
  • upload_module_outliers.R: added dim check for counts before return(); included counts in returned list. view
  • upload_module_outliers.R: temp disabled counts in return() view
  • upload_module_computepgx.R: added dim check for countsRT, countsX, samples, contrasts. view
  • upload_module_computepgx.R: disabled 'skip normalization' and 'do.normalization' view
  • upload_module_outliers.R: added counts in returned list; fixed imputedX to also return counts. view
  • Update upload_server.R: added countsRT as counts from upload_module_outliers_server view
  • upload_module_outliers.R: added dbg("input$scaling_method") view
  • Added step for detection of negative values view
  • Refactored imputedX(); Disabled median centering in normalizedX(); Temp disabled techn/biol effects corr; Disabled omission of zero at quantile norm. view
  • VERSION view
  • Disabled params view
  • Renamed norm functions; Moved check for negative values into normalizedX. view
  • Disabled global_scaling; added check box for quantile normalization; added normalization methods view
  • Added new menu for correction of biological and technical factors view
  • add option to select contrast in report view
  • minor fix for passing comparisons param view
  • update readme with env variables view
  • Refactorings to upload_module_outliers.R view
  • Refactorings to upload_module_outliers.R view
  • Corrected typo in dbg message in normalizedX() view
  • fix: retrieve counts values view
  • fix: counts QC with negative counts values view
  • Added dim check in upload_module_outliers.R; Fixed retrieval of counts; added corrected1 in upload_server.R view
  • Added check for zeros and negative values; add to NA values; add 1e-10 to 0 to enable log normalizations view
  • Commented on neg values view
  • Refactored imputation step in upload_module_outliers.R view
  • GENETEST: t-tests and limma in upload_module_computepgx.R view
  • Changed parameters of boxplot in upload view
  • Fixed missing value plot at upload when no missing values in the data view
  • More fix in the missing value plot; Restored LogCPM+quantile Norm as default; Restored outliers detection accordion_panel view
  • Added gx.imagemap to missing value plot at upload view
  • Expanded datatypes: LC/MS proteomics; SNR view
  • Removed Accordion Panel for Technical/Biological factors correction; Refactored imputation and normalization step; added 1e-20 to avoid zeros after normalization; added checks for zeros, negs, NAs, Inf. view
  • Removed excessive checks. view
  • remove forced log-transform reversal if counts < 60 view
  • feat: move qc/bc UI to server view
  • doc: added qc/bc plots info view
  • added +1 or +1e-20 depending on normalization view
  • style: more space for next/prev buttons view
  • added +1 or +1e-20 depending on normalization view
  • fix height of wizard container view
  • add margin to outlier module view
  • clean up view
  • Added prior +1 or 0 view
  • resolve merge conflicts view
  • attempt to fix normalization plots (revert if needed) view
  • work in progress view
  • resolve merge conflict view
  • added na=TRUE to min and max in density plots view
  • Fixed RUV name view
  • bring dataset description as first step in dataset uploda view
  • pass organism to counts check view
  • do not reset organism when starting a new upload as resetting will overwrite default human view
  • clean up view
  • minor fix for popup displaying incorrectly view
  • add basic skeleton of futures prototype view
  • style: better norm plot spacing view
  • comment out prototype of extended tasks due to issues when running annotation hub view
  • added user input box to treat xxl features as NAs view
  • VERSION view
  • add download handler for html file (we might need to refactor if images are not in svg) view
  • Code Cleaning view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • test: grab plot settings view
  • Refactored BC step; Not run SVA,RUV,t-SNE if there are NAs; Fixed coordinates to be PC1 and PC1 at BEC plots; Renamed NPmatch to NPM; Added las=1 in BC plots view
  • Update VERSION view
  • Update VERSION view
  • feat: working settings download view
  • split pgxcompute into two modules: basic backbone view
  • clean up computepgx view
  • do not lock upload at start, as we have all inputs already defined view
  • feat: move sett to ui-utils view
  • fix: hide genelist view
  • fix: remove word from inputId view
  • feat: left align, all col rename view
  • make layout vertical; attempt to fix selected_organism input update issue view
  • simplify ui pannel and align the input boxes center view
  • apply the same refactoring in computepgx ui view
  • wrap p and div into a div, to keep styles consistent and avoid overwrites view
  • fix merge issues view
  • rename wizard steps view
  • pass data type to batch correction module view
  • ExtendedTask commented out view
  • VERSION view
  • Re-enable ExtendedTask view
  • feat: control popover width view
  • feat: save global params view
  • feat: get metadata table view
  • feat: copy button + references on info box view
  • fix: pass caption with argument name view
  • feat: add tick when copy text view
  • proto: references on info view
  • feat: cog as other elements view
  • feat: heatmap no cexCol=0 with >100 samples view
  • feat: info on second column view
  • feat: info second col view
  • feat: transparent info buttons view
  • style: blank icon view
  • feat: checkbox for plot settings in pdf view
  • hide outlier pannel view
  • feat: move choices to ui builder view
  • Re-instated Skip-norm view
  • feat: new datatype translator view
  • feat: tranlator dictionary view
  • style: ease out transition tick view
  • remove api calls view
  • display conditions in input view
  • minor improvements in UI view
  • feat: use textare view
  • fix contrast selection view
  • integrate visreport without parameters view
  • only select one contrast view
  • fix path argument view
  • feat: dataview proteomics translations view
  • fix issue with updating contrasts upon module reinitialization view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • Pass corrected1 and X to upload_module_computepgx_server view
  • Enable outliers_panels view
  • backbone for extended tasks probe check view
  • WIP: testing MPoC_NA view
  • typo: protein(e) view
  • Renamed proteomics datatype view
  • translate: gene overview view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • remove normalization-related steps view
  • attempt to add probe check in reactive context view
  • render correct probetype message in UI view
  • add ui mnessages to handle ui when ah_task process is running.,.. view
  • fix issues with ui components not correctly displaying message while running ah view
  • unlock wizard in case last state was locked view
  • handle probe type failure view
  • fix: use correct format view
  • feat: update choices view
  • move probetype declaration to HOC upload_server view
  • improve logic to handle probetype state changes view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • fix: check for multiple values if any view
  • feat: collapse vectors view
  • feat: adjust pdf settings height view
  • feat: update pdf settings height view
  • fix: put height into use view
  • feat: update settings pdf height view
  • feat: update settings pdf height view
  • minor fix to output format view
  • WIP view
  • WIP view
  • feat: clustering and expression settings calendar view
  • refactor generate report ui to accept selected pgx from loading table view
  • WIP view
  • fix: change list names view
  • feat: settings pdf bigger width view
  • WIP view
  • feat: no parent inputs + new cluster dictionary entries view
  • nothing particular view
  • correct progress set -> inc view
  • update view
  • feat: new info structure view
  • merge master view
  • Refactor to accomodate normalization and imputation changes view
  • example: clustering board view
  • feat: use external link button instead of info view
  • feat: disable settings on pca/tsne view
  • feat: hide
    s on tab change view
  • WIP view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • Refactor returning objects view
  • update: added preview example thumbnails. prototype working. view
  • fix: sidebar issues view
  • feat: pheno distribution info view
  • add alert if visreport not installed view
  • feat: compare datasets compute button view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • Renamed datatype to Proteomics view
  • Correct typo in succefully view
  • Remove limma-voom as default; added impX argument view
  • Added impX argument view
  • Added impX argument in computed_pgx view
  • General refactorings view
  • fix: if tick is present, do nothing view
  • fix: typo view
  • Refactorings + add norm_method view
  • fix: pass value not reactive view
  • Added norm_method view
  • WIP view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • add selection choice for comparisons all/selected view
  • resolve merge conflict view
  • Remove fgsea (temp) view
  • Refactorings view
  • Fixed BC plots at upload view
  • feat: save lower datatype view
  • Update version view
  • feat: dataview plot labels for proteomics view
  • typo: protein(e) view
  • translate: gene overview view
  • feat: more translation for dataview view
  • merge MPoC/MPoC_NA into MPoC_NA view
  • feat: upload tranlation and defaults for proteomics view
  • Fix Average Rank Plot to handle NAs view
  • correct BS layout view
  • Rename proteomics datatype to LC/MS proteomics view
  • Use abundance.csv for proteomics data view
  • Added string protein in message view
  • Specified datatype LC/MS proteomics view
  • convert to plotly only if Iheatmap object view
  • WIP: simplify reactivity example for plot_compare1 view
  • docs: plots info buttons view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • simplify ExtTask returning probetype; remove dependency ah_task parameter to computePGX view
  • style: add padding left to references view
  • add input_recap2 at compute page view
  • only 1 clust.method; remove evaluation/scoring of BC methods (faster, not needed now) view
  • restyling compute page view
  • docs: featuremap info buttons view
  • rename steps; add info at first page view
  • add alert if probetype task is not finished or has error at compute step view
  • add alert if probetype task is not finished or has error at compute step view
  • docs: expression info buttons view
  • docs: missing arguments on featuremap view
  • resolve merge conflicts from MPoC_NA view
  • add methods view
  • Fix BC + Refactorings view
  • Resolve conflicts view
  • Rename datatype to Proteomics view
  • docs: correlation info buttons view
  • Fix Distance matrix in presence of NaN view
  • Fix Distance matrix in presence of NaN view
  • docs: biomarker info buttons view
  • Checks view
  • Conform pos and F for Geneset UMAP view
  • Fix key view
  • Remove unexisting function view
  • docs: enrichment info buttons view
  • Fix correlation barplot and table view
  • add shiny.i18n to Dockerfile view
  • Add chr map into Diff.Gene.Expr. table view
  • Use impX for glasso::glasso around gene view
  • Fix appearance of AvgExpr in DGE table view
  • Remove dbg messages view
  • Remove impX view
  • feat: rename abundance/counts.csv view
  • datatype and filename view
  • Fix Correlation UMAP view
  • Fix Correlation visuals view
  • Fix Volcano geneset signature if F has NAs view
  • Change outlier label box view
  • Rephrasing check box view
  • Rename y-axis barplot top DEG view
  • Fix AVG and SD for Table count view view
  • Add Corresponding Gene Info for UNIPROT ID for Proteomics data view
  • Fix AveExpr0 and AveExpr1 in Geneset table view
  • Remove Dbg messages view
  • Add ssgsea and fgsea default view
  • Fix ylabs in Dataview board and title of proportion barplot view
  • Rename Counts Data to Data table view
  • Use expression.csv in initial dialog box view
  • Rename y-axis in Cluster samples, Module expression view
  • Rename axes and titles in Cluster samples and Cluster feature tabs view
  • Rename Tab names, Axes in Volcano and MA plots in diff.gene.expr tab view
  • remove new.png snapshots view
  • Tab title and info renaming view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • Renaming view
  • Renaming view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • Rename yaxis view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • Move feature outliers box into Step 3 view
  • Move feature outliers box into Step 3 view
  • fix: dataype/organism NULL crash on new upload view
  • fix NULL empty datatype on new upload view
  • remove *new.png files view
  • switch to v3.4.3.9001 working version view
  • christened to v3.5.0-alpha.1 view
  • clean up view
  • rename module_outliers -> module_normalization view
  • fix: move res_samples initialization view
  • fix: move res_samples initialization view
  • Fix WGCNA corr netw with complete obs view
  • Fix WGCNA module member plot with complete obs view
  • include latest fix view
  • WGCNA: use pairwise.complete.obs view
  • try fix for lexical error translation.json view
  • add debugging shiny.i18n view
  • try fix for lexical error translation.json view
  • try fix for lexical error translation.json view
  • try fix for lexical error translation.json view
  • try fix for lexical error translation.json view
  • fix: language triggers correctly view
  • Automatic translation of datatypes in text by parsing keywords. This replaces the manual entries of whole sentences in translation.json. We also can automatically translate all captions/titles of plots and tables by adding a translate parameter in PlotModule and TableModule. view
  • update dictionary view
  • edit text view
  • vectorize tspan function view
  • adding tspan view
  • translate bs_alert boxes by default view
  • connect menu items to actions view
  • remove new upload button from loading table page; edit board/tab titles view
  • add logCPM view
  • Revert "Automatic datatype translation of text by parsing keywords. " view
  • fix counts.csv reactivity in case NULL view
  • Recoded after revert of PR view
  • Recoded after revert of PR view
  • rework wizard view
  • add translation keywords view
  • update view
  • add capitalized view
  • add log2p1 view
  • merge MPoC view
  • finished working version view
  • Fix Biomarkes - Feature-set Ranking plot for Proteomics view
  • Update view
  • add plots at counts and samples wizard steps view
  • fix: start wizard in locked mode view
  • reorder inputbox view
  • start beta series v3.5.0-beta.1 view
  • version: v3.5.0-beta2 view
  • fix: set display none view
  • fix: select correct column to highlight individual gene view
  • feat: use correct font on plotly hover tooltip view
  • update gitignore view
  • fix: crash when length()>1 in if view
  • fix method error; reinstate ComBat as auto-ComBat view
  • feat: prefix gene symbol for selectInput if feature is not symbol view
  • change message view
  • change plot title view
  • make drop menu font larger view
  • edit text to fit rna/proteomics view
  • improve logging of users request in pgx compute crashes via hubspot tickets view
  • docs: signature info buttons view
  • docs: wordcloud info buttons view
  • docs pathway info buttons view
  • refactor and clean up after testing with login-code authentication view
  • do not return response view
  • clean up view
  • fix columns view
  • fix lables view
  • fix datatype labels view
  • edit labels view
  • docs: loading info buttons view
  • style: hover template tsne loading plot view
  • fix: typo view
  • attempt to handle run time errors and traceback with hubspot tracking view
  • docs: compare info buttons view
  • WIP view
  • add js paramter for tspan view
  • remove dbg output view
  • remove dbg output view
  • refactor module loading. maybe more efficient view
  • remove unused code view
  • fix: species inputselect choices view
  • rename button view
  • add button action on header dataset name view
  • working version 9001 view
  • feature: fix crash and allow multiple csv files at upload view
  • decrease prior to 1e-4; add reference normalization (needs playbase update) view
  • v3.5.0-beta4 view
  • enable org.eg.db instead of AnnotHub view
  • enable org.eg.db instead of AnnotHub view
  • improve handling of failed BC method view
  • disable dual NA heatmap view
  • add MSnbase view
  • comment out TMM view
  • fix: select genes view
  • protect against negative counts view
  • resolve merge conflicts view
  • resolve merge conflict view
  • add shadow for better look view
  • delete duplicated file view
  • increase margins view
  • align dropdown menus view
  • use abbreviation in making contrast names view
  • adapting for 24.04 view
  • translate: apply tspans where necessary view
  • add DESCRIPTION file, prepare for new Dockerfile view
  • new docker file for 24.04 view
  • add new file view
  • update view
  • delete backup files view
  • edit view
  • update view
  • WIP update view
  • feat: enables upload of paramsRData file for debugging view
  • add squash target view
  • Add feature_name in gene_info box view
  • Uncheck option Convert probes to symbols as default view
  • add files to create alpha docker (based on new playbase image) view
  • remove squashing. no need. view
  • add glob pattern in COPY if file not exists view
  • correct if statement view
  • fix: translate caption2 first view
  • update view
  • update version view
  • fix: allow upload of old-style contrasts (needs updated playbase) view
  • Update upload_module_preview_contrasts.R view
  • feat: count total comparisons from FC file view
  • prepare ui new data type, add datatype at detect_probetypes view
  • Add p-value to DGE table (MPoC request) view
  • Add p-value to DGE table (MPoC request) view
  • Resolve conflict view
  • Resolve conflict view
  • fix: small errors at contrast making view
  • fix: take out others & better reset of bucket view
  • fix: take out others & better reset of bucket view
  • fix: take out others & better reset of bucket view
  • edit layout for tighter space view
  • update translation.json to support metabolomics view
  • refactor i18n server logic to allow translation for metabolomics (attempt) view
  • add ui component to select probe type for metabolomics (attempt) view
  • Added option to show meta (nominal) p-values on the Volcano Plot view
  • pass probe_type to detect_probetypes to match the current logic, displaying probetype at lsat comptue step view
  • fix minor issue with probetype causing a crash view
  • pass probe_type to pgx computation view
  • fix correlation board to work with uniprot rows && improve plotly subplot view
  • improve layout spacing view
  • improve/refactor gene info box view
  • attempt to fix computation spinner by adding the right selector view
  • clean up view
  • fix default selection view
  • fix plots for compound feature names view
  • change option labels to match new gene filtering view
  • improve plot layout view
  • improve plot layout view
  • improve margins view
  • improve margins view
  • fix feature-UMAP for duplicated symbols && simplify code and options view
  • limit message panels at startup view
  • Fix DGE table for top10 up/down features; Remove option to show inidivual qvalues view
  • Fix DGE table for top10 up/down features view
  • Resolve conflict view
  • Show (optionally) p-values in DGE table view
  • update view
  • style: plotly hoverlabels view
  • Disable p-values as local option in Volcano plot view
  • update view
  • version beta5.9002 view
  • Add Warning message for nominal p-values view
  • update view
  • remove DEV code pieces. new DEVMODE option parameter. view
  • add DEVMODE parameter in OPTIONS. Upload params.RData only possible in DEVMODE=TRUE view
  • Renaming view
  • Optionally show p values in Volcano view
  • Add meta.p as user option; reorder columns in DGE table view
  • feat: label by symbol view
  • set explicit navbar height view
  • fix: wikipathways do not require meta.go view
  • style: decimal places view
  • fix: missed : view
  • Renaming view
  • fix/feat: select label type on volcano plots as feature or symbol view
  • make buttons smaller view
  • rename to Home view
  • try new action menu (commented out) view
  • add description view
  • fix stackedbarplot for genes with low frequency view
  • Restore optional p values in DGE table view
  • fix: keep as dataframe when subsetting one column view
  • merge view
  • remove DEV if statement view
  • put UMAP plot first view
  • Fix Feature table in cluster genes view
  • fix: if SBGN errors, try without gene data view
  • set labels default by probe view
  • Improve readability view
  • Fix names and label.names view
  • feat: probe filter defaults for proteomics view
  • feat: use YAML file for defaults view
  • feat: DEFAULTS.yml view
  • Add: checking of organism and datatype in ExtendedTask view
  • Disable binarization view
  • Added na.rm=T view
  • Account for warning in dense regularized network - increase specificity. view
  • Trigger WGCNA recomputation when users selects different parameter values view
  • Swapped logFC and FDR box options positions view
  • Added na.rm=TRUE as needed view
  • update view
  • fix issue with flexbox containers overflow issue with fill item view
  • Added na.rm=TRUE as needed view
  • Added na.rm=TRUE as needed view
  • Added na.rm=TRUE as needed view
  • Added na.rm=TRUE as needed view
  • Added na.rm=TRUE as needed view
  • Added na.rm=TRUE as needed view
  • Added na.rm=TRUE as needed view
  • refactor of signature board for handling newer annotation and PTM dataset with selection on symbols view
  • change to use organism specific gene info using getOrgGeneInfo view
  • update syntax view
  • add weblink CSS view
  • change names/label.names view
  • version up 9003 view
  • Added na.rm=TRUE as needed view
  • update view
  • fix typo view
  • Update README.rst view
  • refactor board to use playbase plotting functions view
  • improve margins in plot layout view
  • fix: transpose error view
  • descrease title size view
  • move weblink. paste after name. view
  • move weblink; rename header view
  • fix for "unused arguments (features = df$pathway, showscale = TRUE)" view
  • implement fix to go pathway view
  • fix: dimension error, matrix not provided view
  • version 9004 view
  • fix selection and other small things view
  • take out datatype dependency view
  • Rename Probe filtering to Feature Filtering view
  • refactor CompareBoard view
  • small cleanups view
  • small cleanup view
  • version beta6.9001 view
  • fix: if error view
  • fix: if error view
  • fix for length of 'dimnames' [1] not equal to array extent in biomarker/featurerank biomarker view
  • small UI changes view
  • small UI changes view
  • fix: disable tooltip on plotmodule title view
  • fix issue with connectivityBoard to work with non-gene features as in PTM proteomics view
  • fix: match always with human_ortholog view
  • fix: call correct colMeans method view
  • fix: fix row selection, fix color limits view
  • simplify code. collapse to human gene earlier view
  • insert centrality code (not yet working) view
  • move update of species selectInput list to server view
  • add back rm.locks view
  • fix: crash on show pvalue view
  • remove docker alpha build; make alpha default view
  • Added links to phosphoELM for proteomics data view
  • version beta7 view
  • version beta7 view
  • Allow custom annotation columns in the counts.csv file which can be shown in the DataView/DataTable with a checkbox 'show full table'. This allows users to add extra feature annotation columns. Any columns that overlap with OPG will overwrite our annotation so in principle this can be used for custom annotation of non-supported organisms, or if users want to use a specific annotation view
  • fix merge conflict view
  • fix compare datasets for datasets with non-symbol rows (PTM) view
  • correct rename_by call view
  • correct dataview view
  • fix conflicts in ExtendedTask view
  • add new release documentation view
  • v3.5.0-beta8 view
  • cleanup view
  • update document view
  • add translation view
  • fix: remove reactivity on organism slect view
  • update view
  • add quarto view
  • fix parameter (was inverted) view
  • change call to allSpecies view
  • add lato fonts view
  • no cache as default view
  • assign metabolomics as beta datatype view
  • set append to default view
  • add default datatype parameter view
  • add metabolite annotation information and refactor geneinfo_data reactive (needs review) view
  • fix: color ALL significative genes view
  • fix: crash if annot_table is NULL view
  • add Docker.update: only update omicsplayground and playbase code, no dependencies view
  • correct path view
  • beta-version v3.5.0-beta9 view
  • add extra path for visreport view
  • move check of maximum datasets to upload button view
  • version beta9 view
  • RNAseq as default view
  • remove add quantile; add CPM+QN as method view
  • remove dbg comment view
  • feat: install quarto for current cpu architecture view
  • remove commented line view
  • fix strange reset of upload wizard when clicking final compute view
  • remove dbg view
  • remove dbg lines view
  • remove dbg lines view
  • v3.5.0-beta10 view
  • feat: translate methods text view
  • small adjustments to featuremap info texts view
  • remove color_up_down option view
  • fix feature-set ranking plot view
  • fix error with enrichment_plot_freq_top_gsets dimentions passed to stacked barplot view
  • fix issue with volcano genesets now showing any gene in old and new datasets view
  • rename file to keep consistency in filenames view
  • add gene table to enrichment table (important for metabolomics) view
  • add limma in batch correction methods view
  • lower case limma view
  • lower case limma view
  • lower case limma view
  • put links after term view
  • add link to genesets view
  • add link to genesets view
  • style: dataview use omics palette colors view
  • style: clustering use omics palette colors view
  • fix: remove NAs in mean view
  • fix issue when subsetting rnaX (pp had NAs) view
  • simplify invite check view
  • hide WGCNA and PCSF for metabolomics data view
  • fix issue with NAs as names of vector and crashing top enriched geneset plot view
  • feat: metabolite defaults for testgeneset view
  • remove gene_names and pass feature view
  • fix: NA rownames use character "NA" to not break plot view
  • gene equals selected table rowname view
  • rename pathway name to a more known version (TCA cycle) view
  • feat: updated plotmodule cards view
  • fix: grab gene names from rownames view
  • volcano plot prototype with feature names as labels view
  • refactor MA plot to allow labels to be feature names view
  • fix: place id in order to trigger the download button conditional panel view
  • style: plotmodule modal cards view
  • feat: static volcano plots view
  • feat: download tables options: csv/excel view
  • updated DESCRIPTION view
  • feat: expression board now works entirely on rownames (instead of symbol/feature) view
  • feat: add excel download to plotmodule view
  • typo: change info view
  • set default mapping to rownames instead of symbol ( genes_selected return symbol which is a problem, needs refactoring) view
  • return rownames instead of symbol in genes in geneset observer; solves several plot problems view
  • feat: multivolcano expression 2 static view
  • return rownames (and not symbol) from getAllContrasts to match reference ids view
  • refactor code to get ids from getAllContrasts and directly map that to pgx$genes for reliability view
  • remove old code view
  • fix: pass thresholds to static volcano view
  • minor typo fix view
  • remove symbols from id mapping in expression_plot_volcanoMethods as we now use rownames view
  • clean up view
  • enrichment static volcano view
  • remove unnecessary line view
  • enrichmentmethods static volcano view
  • DGE tab: 1. Change label from FDR to P-value if 'Show p-value' option is checked. DGE table reports only meta.p and p-value columns if option is checked. view
  • Fix show of p/q in table view
  • Fix show of p/q in table view
  • Fix show of top10 up/down features if less than 20 features are available view
  • update view
  • Fix show of top10 up/down features if less than 10 features are available view
  • Fix DGE table filtering depending on FDR or P-value metric view
  • update view
  • improvements to ticketing system in case pgx is not loaded and user email is not defined view
  • also check if element PGX$name is not null before assigning pgx not loaded to variable view
  • remove dbg view
  • move user email check to utils and not server view
  • Dynamic ylab p/q in Volcano plot Methods view
  • update view
  • Dynamic ylab p/q in Volcano plot All view
  • update view
  • Fix p-value on y-axis in Volcano Methods view
  • Fix -value on y-axis in Volcano all contrasts view
  • update view
  • Add info for WGCNA Module-Trait Relationship Heatmap view
  • update view
  • add option to display clustered heatmap with feature, symbol or name view
  • increase horizontal spacing between widgets; shift checkbox input to end of panel view
  • fix for ptm data view
  • update label instead of redrawing whole input element view
  • update playdata as well view
  • fix 898 where custom features are not in rownames view
  • be able to list single gene in UMAP plot view
  • fix: just add available genes view
  • improve warning in case probetype check fails for metabolomics view
  • minor fix to assign error to detect_probetype in case probe do not match metabolomics probetypes view
  • correct handle probe type matched with success view
  • fix: label proper genes view
  • simplify code; improve message to user when no matches across all legacy organisms view
  • rename to ggVolcano view
  • merge master view
  • feat: hubspot check view
  • feat: move hubspot check to a function view
  • update messages (take out summer message) view
  • prototype of global labeltype works (initialized when PGX is loaded) view
  • apply same solution to clustering board view
  • change dot/label size for modal view
  • add notification UI view
  • Revert "feat: hubspot data check" view
  • fix playbase::ggVolcano not showing correct labels for metabolomics view
  • move labeltype logic to trigger at every dataset change view
  • fix detect_task error #1014 view
  • remove labeltype selector for clustering splitmap (done globally) view
  • add global ui control in settings kog wheel view
  • fix info order and titles view
  • redesign UI elements: bring geneset volcano upfront view
  • smaller font view
  • edit plots view
  • add visInteraction view
  • version v3.5.0-beta11 view
  • decrease number of genes in plot view
  • fix sig and fc thresholds view
  • feat: place connector on outside repo/folder view
  • add new option view
  • control missing option view
  • Added creator in table view
  • fix grey dots due to incomplete selection view
  • use rownames view
  • feat: add JS option to tablemodule view
  • add js option to upload table view
  • fix: use grepl for proteomics data detection view
  • remove dbg statement view
  • rename view
  • feat: add autoclose to cog dropdown view
  • feat: cog menu remove weird artifacts view
  • fix receive/sent tables not showing view
  • beta12.9001 view
  • fix: call a visNetwork to initialize view
  • update labeltype to reactive component; add labeltype to dataview view
  • fix typo: add missing closing parentheses view
  • add labeltype switch in dataview search_gene selector; clean up features definition based on data type (needs review) view
  • add labeltype to observeEvent and fix issue with pre_labels being NA when symbol view
  • remove browser view
  • fix error missing value where TRUE/FALSE needed in geneinfo module view
  • add bigdash to update dockerfile view
  • update labeltype input selector when datasets is changed view
  • feat: dockerfile update, add flags view
  • style: signature to omic palette view
  • typo view
  • style: intersection to omic palette view
  • remove commented lines view
  • test: add test dependency view
  • fix req() isTruthy bug when NA in dataframe view
  • binarize continous phenotype variables at median so comparisons can be made view
  • save connectivity results of USER sigdb to avoid recomputation view
  • save connectivity results of USER sigdb to avoid recomputation view
  • fix color on compare datasets umap view
  • fix: add i18n to dev boards view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • snap review view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • snap review II view
  • remove signature from snapshot view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • rename snapshot test utils from build-test-push to snapshot-test` view
  • fix typo git mv view
  • fix if statement errors view
  • v3.5.0-rc1 view
  • fix geneinfo ortholog error view
  • add sf package; rename functions NOTUSED view
  • feat: capture error message next to traceback view
  • feat: no title on ggplot volcano plots view
  • feat: grab tab/general settings view
  • add file pattern view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • snapshot review view
  • fix: return to defaults if not pairwise view
  • fix: state function argument view
  • feat: gtest defaults proteomics/others view
  • handle null info view
  • add packages listviewer view
  • add basic template for label_type general annotation view
  • bump to v3.5.0-rc2 view
  • fix issues with matrices with duplicated columns; align labeltype with pgx$genes columns; prototype playbase::probe2symbol in dataview view
  • Barplot of number of detected feature per sample view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • Update dataview_plot_totalcounts.R view
  • Update dataview_ui.R view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • feat: avoid logging repeating errors view
  • snapshot: add datatype view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • snapshot review view
  • test board name change view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • fix: remove duplicated argument view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • fix: compare for multiple selection on samples filter view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • snapshot review view
  • feat: new error message view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • fix: check uni-node graph view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • correct message text view
  • refactor and clean-up labeltype code to use probe2symbols view
  • delete snaps linux-4.1 view
  • fix selection of points when duplicated symbols; clean table view
  • revert corrected2 solution from previous wizard-bug; seems not needed anymore view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • fix issue with label names in volcano plot view
  • cleaning up view
  • fix several issues in labeltype conversion; improve naming when selecting labeltype options view
  • refactor VolcanoMethods to new system; fix ggVolcano (static) view
  • clean up view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • fix: feature umap labels view
  • feat: correlation analysis use labeltype view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • add reactive context so that tests and single board launch have labeltype defined view
  • update snaps crashing due to missing labeltype view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • move graph options to plot & graph/table options to sidebar view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • move weblink after entry view
  • update view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • fix req() needed view
  • fix req() needed view
  • fix merge error view
  • fix merge error view
  • add manually specified ComBat and limma; needs updated playbase view
  • v3.5.0-rc3 view
  • feat: compare plots labeltype view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • feat: compare fc plots labeltype view
  • pass labeltype to compareboard view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • snapshot review view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • final review view
  • feat: detect brush for gene umap view
  • compare: set default for labeltype view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • snapshot review view
  • fix: go-to upload tab view
  • fix: keep pgx organism view
  • cleanup code view
  • cleanup code view
  • feat: bring back phenotypes umap view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • Code cleaning view
  • remove unnecessary line view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • add clear/reset recompute_pgx view
  • fix: geneset table view
  • add clear/reset recompute_pgx view
  • add clear/reset recompute_pgx view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • fix: check correct tag view
  • feat: move wizard to server view
  • pass server argument view
  • snapshot review view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • final snapshot review view
  • add compute input reactive to switch for computePGX view
  • add compute input reactive to switch for computePGX view
  • make sure we reinstall wizardR at update view
  • fix umap not appearing if counts has zeros (solution adding prior) view
  • add median normalization view
  • fix: match, drop + Matrix view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • fix: add req to avoid error message view
  • add symbol column for map_probes view
  • fix: check dimensions of table view
  • autodetect of metabolomics probetype; remove probetype selectinput view
  • version v3.5.0-rc3 view
  • bump to v3.5.0-rc4 view
  • fix: do not check names view
  • update version v3.5.0-rc4 view
  • feat: add req for data change view
  • feat: normalization defaults for proteomics view
  • fix: check that decrypted_cookie is not null view
  • feat: re-inforce cookie checks view
  • fix: remove NAs when checking any view
  • fix: drugconn drop FALSE view
  • fix: remove NA gsets view
  • set pdf settings to TRUE view
  • add extra is.na check view
  • feat: add req to avoid error on dataset change view
  • change text view
  • fix reactive labeltype. needs update/PR in playbase. should not pass reactive to regular plot function view
  • fix for issue #1152. hilight not found error view
  • wip view
  • fix: use reactive val view
  • feat: validate number of samples view
  • fix: validate length of inputed phenotypes view
  • feat: disable cmap for metabolomics view
  • fix: drop false for edge case view
  • feat: just check error message for duplicates view
  • feat: bring back bin update for cytometry plot view
  • fix: match pmarkers to symbol view
  • fix: match to symbol view
  • feat: remove server view
  • feat: just update pmarkers when needed view
  • remove browser view
  • clenaup view
  • remove unneeded length view
  • fix: remove duplicated title argument view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • feat: turn is_compute false on dataset change view
  • feat: display intial board state on dataset change view
  • feat: use same matrix that will be subseted view
  • Fix ylab dist from axis view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • fix: make sure genes are within symbols with intersect view
  • snapshot review view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • snapshot review view
  • fix: if no rows skip view
  • fix: check pmarkers view
  • feat: specify library view
  • version update 241011 view
  • version update 241014 view
  • version update rc5-241014 view
  • wip: use pgx$samples view
  • feat: handle no HO case view
  • feat: control samples/counts no match for umap plot view
  • add toupper view
  • move nrow==0 check view
  • Update featuremap_plot_table_gene_map.R view
  • set server=TRUE view
  • feat: add validator view
  • feat: add req view
  • feat: make sure row is selected view
  • snapshot review view
  • feat: use samples tables instead of Y view
  • fix: include _ and drop FALSE view
  • feat: add req view
  • fix: use correct variable view
  • Update pathway_enrichmap.R view
  • update version view
  • save-files-at-upload view
  • feat: save raw_dir to error ticket view
  • feat: raw_dir global to access it on error handle view
  • feat: make sure raw_dir is initiated view
  • feat: add raw dir view
  • new version view
  • quickfix: move up data save and raw dir view
  • feat: handle single k case view
  • feat: add validator on cluster heatmap view
  • fix: comment unused code that produced error view
  • fix: parse txt with new format view
  • fix: eBayes on try-catch view
  • fix: must check on colnames view
  • fix: just check rownames Y, not on names y view
  • feat: labeltype to average rank plot view
  • feat: remove source from labeltypes view
  • fix: check outliers on subseted matrix view
  • fix: use default detectOutlier filter view
  • bump version RC6 view
  • fix: make path relative not absolute view
  • feat: add path to cookies view
  • fix: move path to correct cookie endpoint view
  • fix: impute to compute pca view
  • fix: add validator + drop false for good practice view
  • Add WARNING message about DGE testing in presence of NAs view
  • fix: add req view
  • add update packages view
  • move new packages view
  • fix: sel is the character vec itself view
  • fix: drop false for single case view
  • version bump view
  • Added link to Readthedocs methods on normalization view
  • Update upload_module_normalization.R view
  • fix: add shiny::req view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • Polishing view
  • Polishing view
  • Include valid pheno for dim red; added shiny::validate::need to inform user. view
  • style: color and hover of info button view
  • style: info button on final step view
  • add TileDBarray view
  • feat: save table on upload view
  • version update v3.5.0-rc6+master241028 view
  • version update v3.5.0-rc7 view
  • Added link to readthedocs normalization section; batch-correction; link to imputation blog. view
  • Remove unused code view
  • fix: add req to prevent error view
  • feat: match on symbol, not gene_name view
  • feat: bring back <all> if no other option available view
  • feat: validate and inform user view
  • fix: display correct pathway database view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • snapshot review view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • snapshot review view
  • fix: make sample deterministic view
  • fix: add drop = FALSE view
  • fix: add drop = FALSE view
  • fix: more drop = FALSE + data re-shape when 1 sample view
  • release 3.5.0 view

v3.4.3 (2024-07-22)

  • add dbg statements for refactoring view
  • attempt to create HOC for selected gene in expression board view
  • minor fix for reactVal calling view
  • add missing logic to define sel.genes when no gene/geneset is selected view
  • add missing parameters to define genes when no gene in table is selected view
  • connect HOC to volcano to highlight genes view
  • clean up genes_selected code in expression plot view
  • clean up dbg statements view
  • clean up unused function arguments view
  • clean up redundant reactivity in MA plot view
  • remove unused arguments for MA plot view
  • attempt to pass highlight genes from HOC to volcano (needs playbase refactoring) view
  • ability to highlight gene (order needs to be fixed) view
  • fix issue with incorrect order of feature names view
  • attempt to add selected gene to volcano>methods view
  • when a gene is selected, do not color all significant view
  • clean up unused code due to refactoring and HOC in volcano all view
  • clean up volcano methods; pass HOC component to plots view
  • volcanoall now displays selected geneset view
  • volcanomethods now displays selected geneset view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • feat: custom genes on gene umap filtering view
  • fix: replication + allowed methods view
  • git version tagged v3.4.0 view
  • update readme with env variables view
  • Revert "update readme with env variables" view
  • version v3.4.1: disable xbioc, all annothub view
  • fix: handle 1 geneset table view
  • v3.4.1 view
  • feat: sanitize spaces on input_code view
  • docker: add mpoc dockerfile/makefile view
  • Revert "docker: add mpoc dockerfile/makefile" view
  • docker: install matching playbase view
  • pass updated custom.genesets to pgx.compute view
  • attempt to fix error in batch-effects correction plot view
  • fix: remove coloring view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • update snap view
  • style: -1/+1 color palette view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • cleanup: remove un-used temp.js code view
  • fix: use proper params view
  • clean: remove un-used observers view
  • fix: add rules when objects in DOM view
  • fix: add rules when object in DOM view
  • clean: un-used code view
  • feat: remove web-share view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • fix: sidebar issues view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • remove dbg statements view
  • tag plot.pcsf as NOTUSED; to be removed view
  • remove offending read matrix code view
  • merge master; resolve conflicts view
  • v3.4.2 view
  • fix color bug at welcome screen view
  • fix startup modal size/color bug view
  • update view
  • v3.4.2 view
  • switch to working version v3.4.2.9001 view
  • revert to 3.4.2 for docker rebuild view
  • add file view
  • updated view
  • switch to dev version 3.4.2.9001 view
  • remove images view
  • fix: correct inverting log transform with prior view
  • feat: check logarithm and show confirmation dialog at counts upload view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • set negative values to zero and issue warning view
  • delete new.png view
  • Snapshot test failed: use snapshot_review('snapshot/') (GHA) view
  • v3.4.3 view
  • fix path view
  • change message view