Release Notes

Version 0.1.22: September 11, 2025

General:

  • Improvements in define clones report
  • Some report file sizes bugfixes
  • Added filtering options in collapseDuplicates report
  • Added option to mask positions 5’ and 3’ in the sequence_alignment as part of the collapse duplicates report

Version 0.1.21: April 3, 2025

General:

  • Added lifecycle dependency
  • Fixed duplicate counting for singletons.

Version 0.1.20: March 31, 2025

General:

  • Fixed duplicate counting for singletons.

Version 0.1.19: November 25, 2024

General:

  • Fixed defineClones no existing c_gene for TCR data.

Version 0.1.18: November 25, 2024

General:

  • Fixed CollapseDuplicates to annotate isotype information in c_region or c_primer fields in the c_call field when c_call is NA.

Version 0.1.17: October 14, 2024

General:

  • Fixed bug in single-cell QC report when database was empty.
  • Fixed bug in collapseDuplicates to provide as numeric field “duplicate_count” and “consensus_count”.

Version 0.1.16: May 29, 2024

General:

  • Fixed bug plotting mutation frequency.

Version 0.1.14: April 21, 2024

General:

  • Fixed bug to run Dowser lineages with raxml
  • Added saving RDS object for Dowser formatted clones and trees

Version 0.1.13: March 12, 2024

General:

  • Improved defineClones report and added mutation frequency calculation
  • Fixed bug that eliminated light chains from bulk or mixed sequencing data from final repertoires.

Version 0.1.10: January 11, 2024

General:

  • Added a copy of fuse.js@6.4.6 to be able to render the reports when there is no internet access.

Version 0.1.5: September 15, 2023

General:

  • Bumped versions to dowser >= 1.2.0, ggplot2 >= 3.4.0 and shazam >= 1.1.2.
  • Updated some reports’ text to be more concise and clear.
  • In the define clones report, added the option to focus the convergence analysis on a particular V gene by setting convergence_vgene. Added the option to specify a threshold for the convergence analysis (convergence_threshold). Added a step to remove light chain only cells after createGermlines.

  • Updated the updated single cell qc report to remove cells with duplicated sequences, not just the sequences.

  • Added additional parameters to the dowser lineages report: num_fields, chain, cell, heavy, collapse, and columns. In the same report, added additional validation steps to check that the fields passed to dowser functions have data. Updated the example input data and the default values of some parameters ( traits: from c_call to day, tips: from c_call to day). Fixed the default value of outname, from define-clones to dowser.

Version 0.1.4: July 31, 2023

General:

  • Aesthetic adjusments to figures and tables.

  • Added conditional evaluation logic to some chucks that don’t need to be evaluated always.

Bug fixes:

  • In find threshold report, updated output path used to save the final tables to use the parameter outname. Changed the output file suffix threshold_summary to threshold-summary.

Version 0.1.3: June 22, 2023

General:

  • Find threshold report. Parametrized distance and threshold subsampling.
  • Define clones project. Added example data, available from url. Made singlecell optional, with default value NULL. species can be set to auto to auto detect from the field species.

Bug fixes:

  • The convergence UpSet was not showing in the report because it was missing a grid.draw statement.

  • Updated the logic in the find threshold report to show the distance to nearest plot only if it is not NULL.

  • Define clones project. Run chucks that require the tissue field only if it exists.

  • Updated figures widths and heights.

Version 0.1.2: June 2, 2023

General:

  • Lineage report. Added parameters: tips, traits. All trees are saved to a .pdf and exported in graphml format.

  • Find threshold report. Added parameters: findthreshold_method, findthreshold_model, findthreshold_edge, findthreshold_cutoff, findthreshold_spc.

  • Define clones report. Limit the size of UpSet plots to 31 sets. 31 is the largest size allowed by ComplexHeatmap::make_comb_mat.

  • Create single page, self contained reports.

Bug fixes:

  • Fixed bug in collapse duplicates that caused the function to fail when all values in d_call were NA.

  • In the define clones report. Added conditional chunk evaluation to chunks of code that don’t need to be executed if only light chain data is available.

  • In the find threshold report. Skip distance plots and findThreshold if all distance values are NA and show a message.

Version 0.1.1: March 8, 2023

Bug fixes:

  • Added the field cell_id to the set of selected columns used to subset the input repertoire in the find threshold report.

General:

  • Use plotly in clone size plots.

  • Resize abundande plots.

Version 0.1.0: February 28, 2023

Bug fixes:

  • Fixed a bug in collapse duplicates report, where it was trying to select columns that sometimes did not exist.

Breaks:

  • Renamed param skip_overlap to skip_convergence in the Define Clones report.

General:

  • Added dependencies: ComplexHeatmap, plotly