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Commits on Nov 10, 2021

• Neo: load somatic variants from VCF instead of DB

  charlesshale

  committed
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Commits on Nov 2, 2021

• Neo: removed redundant wildtype match field

  charlesshale

  committed
  5148840

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Commits on Oct 19, 2021

• Neo: retrieve somatic var subset from DB, handle sample data without HLA alleles

  charlesshale

  committed
  3bc935c

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Commits on Oct 10, 2021

• Added codon multiple method

  charlesshale

  committed
  a0a4632

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Commits on Oct 8, 2021

• Pave: added more unit tests

  charlesshale

  committed
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Commits on Oct 7, 2021

• Pave: removed start & end coding context fields, store codon bases, handle codons spanning exons

  charlesshale

  committed
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Commits on Sep 18, 2021

• Neo: calculate and log other-allele similarity

  charlesshale

  committed
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Commits on Sep 16, 2021

• Neo: added more sample output fields

  charlesshale

  committed
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Commits on Sep 15, 2021

• Neo: tweak neo sample scorer

  charlesshale

  committed
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• Neo: applied latest scoring to sample neoepitopes

  charlesshale

  committed
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Commits on Sep 14, 2021

• Neo: ignore self in recognition check

  charlesshale

  committed
  2637d05

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• Neo: removed all MCF-related logic

  charlesshale

  committed
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Commits on Sep 13, 2021

• Neo: multi-thread leave-one out validation

  charlesshale

  committed
  b0a99af

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• Neo: handle missing TPM data

  charlesshale

  committed
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Commits on Sep 12, 2021

• Neo: ensure transcript expression data exists

  charlesshale

  committed
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Commits on Sep 10, 2021

• Neo:

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  charlesshale

  committed
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Commits on Sep 9, 2021

• Ensembl: removed refs to old config name

  charlesshale

  committed
  88341e0

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• Neo: updated file name

  charlesshale

  committed
  a21a68d

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• Neo: refreshed validation routine for leave-out-allele

  charlesshale

  committed
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Commits on Sep 8, 2021

• Neo: added gene propensity

  charlesshale

  committed
  b9eaaa2

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• Neo: changed expression bucketing

  charlesshale

  committed
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Commits on Sep 7, 2021

• Neo: write expression distributions and change file-naming convention

  charlesshale

  committed
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• Neo: bind expression distribution

  charlesshale

  committed
  c3b13e4

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• Neo: support multiple transcripts in proteome usage

  charlesshale

  committed
  d1c89c3

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• Neo: added recognition similarity

  charlesshale

  committed
  cf38721

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Commits on Sep 6, 2021

• Neo: added transcript expression and analyser

  charlesshale

  committed
  716cc9d

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• Neo: minor fixes to output

  charlesshale

  committed
  2ba8f67

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Commits on Sep 5, 2021

• Neo: process recognition peptides

  charlesshale

  committed
  c977d80

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• Neo: split training from scoring config

  charlesshale

  committed
  7141196

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• Neo: pep-sim output tweak

  charlesshale

  committed
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Commits on Sep 3, 2021

• Neo: write custom fields to scoring output

  charlesshale

  committed
  b05894d

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• Neo: more output for proteome similarity

  charlesshale

  committed
  ff1c3c5

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• Ensembl: generate proteome for non-canonical transcripts

  charlesshale

  committed
  1b8f29d

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• Neo: find ranked proteome peptides

  charlesshale

  committed
  9cc9493

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Commits on Sep 2, 2021

• Neo: removed explicit MCF fields from bind data, can load any additional fields now

  charlesshale

  committed
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