Issues

• Add correction of VAF_AM based on the trinucleotide specific deviations

  bbglab/deepCSA#494 · Filter by author FerriolCalvet opened on Sep 30, 2026

• add plots of proportion of mutations per number of mutated reads per mutation type

  bbglab/deepCSA#493 · Filter by author FerriolCalvet opened on Sep 29, 2026
  1

• report effective depth for adjusted mutation densities

  bbglab/deepCSA#489 · Filter by author FerriolCalvet opened on Aug 25, 2026

• clear outputs and output tables

  documentation
  bbglab/deepCSA#487 · Filter by author FerriolCalvet opened on Aug 20, 2026

• Ensure parallelization is activated by default in positive selection methods

  efficiency-related
  bbglab/deepCSA#482 · Filter by author FerriolCalvet opened on Jul 30, 2026

• add PCA plots for interindividual variability

  Task

  bbglab/deepCSA#480 · Filter by author efigb opened on Jul 7, 2026
  1

  

• bugs to be addressed

  bbglab/deepCSA#477 · Filter by author FerriolCalvet opened on Jun 18, 2026

• HDP signatures failing without clear reason

  bbglab/deepCSA#464 · Filter by author FerriolCalvet opened on May 22, 2026

• code quality cleanup, deduplication, and test coverage

  code-review 👩‍💻
  bbglab/deepCSA#462 · Filter by author m-huertasp opened on May 22, 2026

• Errors with version 1.1.0

  efficiency-related
  bbglab/deepCSA#461 · Filter by author bkohrn opened on May 21, 2026
  5

• Update documentation

  documentation
  Task

  bbglab/deepCSA#455 · Filter by author m-huertasp opened on May 14, 2026
  

• Python scripts optimization

  efficiency-related
  bbglab/deepCSA#450 · Filter by author FerriolCalvet opened on May 13, 2026

• bbgregressions pending issues

  bbglab/deepCSA#442 · Filter by author FerriolCalvet opened on Apr 8, 2026

• Optimize and parallelize adjusted mutation density step

  efficiency-related
  bbglab/deepCSA#434 · Filter by author FerriolCalvet opened on Mar 19, 2026

• Compute depth per chromosome or chromosome arm

  bbglab/deepCSA#428 · Filter by author FerriolCalvet opened on Mar 6, 2026 · Current iteration
  1

• Possible updates

  bbglab/deepCSA#413 · Filter by author FerriolCalvet opened on Jan 20, 2026 · next iteration

• Explore discarding positions based on sequencing depth

  bbglab/deepCSA#410 · Filter by author m-huertasp opened on Jan 9, 2026 · Current iteration
  1

• add more mutation QCs

  bbglab/deepCSA#406 · Filter by author FerriolCalvet opened on Dec 21, 2025 · Current iteration

• report exon number with intervals of protein coordinates

  bbglab/deepCSA#399 · Filter by author FerriolCalvet opened on Dec 9, 2025
  

• Customize annotation of specific mutations

  bbglab/deepCSA#395 · Filter by author FerriolCalvet opened on Nov 24, 2025

• Add validation with pandera

  efficiency-related
  bbglab/deepCSA#372 · Filter by author FerriolCalvet opened on Sep 18, 2025 · next iteration

• Reimplement panel creation and manipulation with PyRanges

  efficiency-related
  bbglab/deepCSA#371 · Filter by author FerriolCalvet opened on Sep 18, 2025 · next iteration

• Pending discussions

  bbglab/deepCSA#359 · Filter by author FerriolCalvet opened on Sep 3, 2025

• PLOTMETRICSQC

  new-feature
  bbglab/deepCSA#336 · Filter by author FerriolCalvet opened on Jul 31, 2025
  1

  

• colors change in subplots

  efficiency-related
  bbglab/deepCSA#328 · Filter by author bkohrn opened on Jul 28, 2025
  1