NEWS.md

In steverozen/mSigAct.server: Shiny Server for Analyzing Mutational Signature Activities

mSigAct.server 0.1.2

Added

• Added a new widget on the VCF uploading page for user to specify filter status when variant caller is not Strelka or Mutect.

mSigAct.server 0.1.1

Added

• Added signature etiology information in the attribution PDF plot.

mSigAct.server 0.1.0

Added

• Added progress message if using bootstrapping to remove some of the signatures in the beginning.

• Added another actionButton "Do another signature attribution" on the attribution results page.

Changed

• Do not create "showSpectraTab", "sigAttributionTab" and "attributionResultsTab" on initialization. Use inserTab instead to show the necessary tabs upon user's action.

Fixed

• Fixed a bug not updating signature etiology table with new R session when user adds more signatures.

• Fixed a bug not showing signature etiology table when user selects another sample with same cancer type and catalog type.

mSigAct.server 0.0.9

Added

• Added contribution percentage of each signature to the reconstructed spectrum in the attribution results.

Fixed

• Fixed a bug not showing thumbnail pictures when user selects the same cancer type and catalog type.

• Fixed a bug not showing thumbnail pictures after restarting R session.

• Fixed a bug in function ReadAndCheckCatalog for checking number of files to be read in.

Updated

• Updated the height for SBS192 plot in renderPlot.

mSigAct.server 0.0.8

Added

• Added informative error reporting when uploading non-VCFs as VCFs.

Changed

• Only show spectra plots for catalog types which have mutations.

• Only show catalog types for signature attribution which have mutations.

• Changed header information in run-information.txt from generated zip file.

• Preserved the file path extensions for example analysis on Strelka and Mutect VCFs.

Fixed

• Fixed a bug when user uploads multiple files in "Upload spectra for signature attribution" page.

mSigAct.server 0.0.7

Added

• Added thumbnail picture for selected sample in "Get signature attributions" tab.

Changed

• Made it default to round the reconstructed catalog for plotting.

Fixed

• Fixed a bug when user uploads a VCF with "unknown" region and proceed to do signature attribution.

mSigAct.server 0.0.6

Changed

• Don't preselect catalog type for signature attribution.

• Hide the "Choose catalog type" UI after using preloaded spectra.

• Removed widget for use to specify the downloadable zip file name.

• Provided a download button for downloading the .zip file generated from uploaded VCF.

• Automatically hide the "Show spectra", "Get signature attributions" and "Results" tab when user uploads new VCF/spectra or run example analysis of VCF or use preloaded spectra.

• Changed the "Search:" label to "Search in signatures ID and etiologies:".

• Changed plan to resolve a future to multicore(not supported on Windows).

• More informative errors for malformed catalog spectra.

Fixed

• Fixed a bug when mutation type change after attribution is not working.

• Fixed a bug of rounding reconstructed catalog.

mSigAct.server 0.0.5

Added

• Added thumbnail pictures for signature attribution results.

• Enabled process VCFs with unknown variant caller.

• Created internal data COSMIC.v3.sigs to select the signatures used for attribution based on user input.

Changed

• Create new temporary directory each time when user generate catalogs and do signature attribution.

Fixed

• Fixed a bug in generating zip archive when the input region is "unknown".

mSigAct.server 0.0.4

Added

• Added signature presence test for SBS96 artifact and rare signatures.

• Added new internal data containing the signatures aetiology information.

• Added data table to show the thumbnail of signatures and aetiology information.

• Added thumbnail pictures for SBS96, SBS192, DBS78 and ID.

mSigAct.server 0.0.3

Added

• Added functionality to do signature attribution.

mSigAct.server 0.0.2

Added

• Added new exported functions for getting signature assignment GetExposureWithConfidence and GetExposureAndPlotToPdf.

• Added new exported function for getting the subset of signatures for a specified cancer type from a specified tumor cohort CancerTypeToSigSubset.

mSigAct.server 0.0.1

• Initial interface for uploading VCFs and generating and downloading zip archive.

steverozen/mSigAct.server documentation built on July 9, 2023, 4:52 a.m.