Version 4.4

Version 4.4.0

This is a minor feature release. It adds the following features:

  • Various updates to the pVACview main interface:

    • Users can no select a row to investigate by clicking on the row

    • Users are now able to select an evaluation for a candidate by clicking on one of three buttons on the right of the candidate’s row.

  • Various updates to the pVACview NeoFox interface:

    • By default, only a subset of NeoFox columns will be shown in order to reduce the width of the table. Additional columns can be enabled by selecting them in the “Column visibility” dropdown.

    • We have added heatmap cell backgrounds to IC50 binding affinity and rank columns.

    • We have added horizontal barplot background to VAF and expression columns.

    • Users are now able to select an evaluation for each candidate.

    • Users are now able to leave a comment on selected candidates.

    • The NeoFox table, including the selected evaluations and comments, can now be exported in TSV and excel format.

by @susannasiebert and @evelyn-schmidt in https://github.com/griffithlab/pVACtools/pull/1137

This release also fixes the following bug(s):

  • A previous change would no longer allow standalone alpha/beta chain DP and DQ alleles. This change would filter out such alleles before trying to combine them into valid alpha-beta-chain pairs. This update once again enables automatic combination of DP and DQ alleles in to alpha and beta chain pairs. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1139

Version 4.4.1

This is a bugfix release. It fixes the following problem(s):

  • Previously, pVACview would add an additional header line to Excel spreadsheets when exporting a TSV. This has been fixed so that the first line in the spreadsheet is the actual header line. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1143

  • One of the pVACview figures used to describe various anchor scenarios has been updated so that the ordering of the scenarios is consistent with other figures and descriptions throughout. Screenshots and documentation has been updated appropriately. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1144

  • The class II pVACview demo data was out-of-date and not reflecting recent updates to the HLA alpha-beta chain handling. This file has now been updated. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1145