Owner

openvax

9 indexed repositories · View on GitHub

pyensembl
Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl

Python · 408 stars
mhcflurry
Peptide-MHC I binding affinity prediction

Python · 275 stars
gtfparse
Parsing tools for GTF (gene transfer format) files

Python · 129 stars
mhctools
Python interface to running command-line and web-based MHC binding predictors

Python · 104 stars
varcode
Library for manipulating genomic variants and predicting their effects

Python · 87 stars
vaxrank
Ranked vaccine peptides for personalized cancer immunotherapy

Python · 67 stars
topiary
Predict mutated T-cell epitopes from sequencing data

Python · 30 stars
isovar
Assembly of RNA reads to determine the effect of a cancer mutation on protein sequence

Python · 26 stars
datacache
Helpers for transparently downloading datasets

Python · 5 stars

Beginner friendly Everything

Open All

Complete context-gallery README names the base-only reproduction command Open

Difficulty 2/5 1-3 hours Newbie friendliness 86/100

openvax/isovar#301 · Opened Sep 18, 2026
Allele-only read collection loads gene annotation solely for logging Open

Difficulty 2/5 1-3 hours Newbie friendliness 88/100

openvax/isovar#295 · Opened Sep 17, 2026
Release tests hard-code 2.3.0 while model fixtures use the current package version Open

Difficulty 2/5 1-3 hours Newbie friendliness 68/100

openvax/mhcflurry#434 · Opened Sep 16, 2026
mhctools | head crashes with a usage dump and exit 2 (BrokenPipeError) Open

Difficulty 2/5 1-3 hours Newbie friendliness 84/100

openvax/mhctools#387 · Opened Sep 15, 2026
A mistyped allele and a missing optional dependency both exit with a traceback Open

Difficulty 2/5 1-3 hours Newbie friendliness 78/100

openvax/topiary#324 · 1 comment · Opened Sep 15, 2026
mhcflurry-predict and predict-scan write progress lines to stdout, corrupting redirected CSV output Open

Difficulty 2/5 1-3 hours Newbie friendliness 90/100

openvax/mhcflurry#423 · Opened Sep 15, 2026
Remove duplicate CleavageInput entry from package __all__ Open

Difficulty 2/5 1-3 hours Newbie friendliness 82/100

openvax/mhctools#358 · Opened Sep 15, 2026
Replace deprecated license classifier with SPDX package metadata Open

Difficulty 2/5 1-3 hours Newbie friendliness 84/100

openvax/vaxrank#446 · Opened Sep 14, 2026
Lint has no rule selection, so it depends entirely on the ruff==0.15.21 pin Open

Difficulty 2/5 1-3 hours Newbie friendliness 86/100

openvax/mhctools#354 · Opened Sep 14, 2026
AGENTS.md describes a deploy.sh and branch that don't exist Open

Difficulty 2/5 1-3 hours Newbie friendliness 88/100

openvax/topiary#317 · Opened Sep 14, 2026
Processing training completion log incorrectly calls the predictor affinity Open

Difficulty 2/5 1-3 hours Newbie friendliness 90/100

openvax/mhcflurry#409 · 1 comment · Opened Sep 9, 2026
Refresh pre-release status text in the Isovar 1.8 documentation Open

Difficulty 2/5 1-3 hours Newbie friendliness 86/100

openvax/isovar#222 · Opened Sep 8, 2026
Release evaluation defaults mislabel the public baseline as 2.0.0 Open

Difficulty 2/5 1-3 hours Newbie friendliness 84/100

openvax/mhcflurry#393 · Opened Sep 6, 2026
Affinity candidate figure assembly does not verify prediction row identity Open

Difficulty 2/5 1-3 hours Newbie friendliness 74/100

openvax/mhcflurry#389 · Opened Sep 5, 2026
Replace deprecated license classifier with SPDX license metadata Open

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

openvax/isovar#205 · Opened Sep 4, 2026
downloads fetch --release fails with custom MHCFLURRY_DOWNLOADS_DIR Open

Difficulty 2/5 1-3 hours Newbie friendliness 84/100

openvax/mhcflurry#384 · 1 comment · Opened Sep 4, 2026
Class1ProcessingPredictor.save subset writes weights and manifest for different model sets Open

Difficulty 2/5 1-3 hours Newbie friendliness 86/100

openvax/mhcflurry#380 · Opened Aug 31, 2026
pVACtools constructs can never carry sibling peptides — undocumented consequence of the identity shape Open

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

openvax/vaxrank#356 · Opened Aug 28, 2026
Processing ablation wrapper forwards training-only DataLoader option to compare-models Open

Difficulty 2/5 1-3 hours Newbie friendliness 82/100

openvax/mhcflurry#378 · Opened Aug 28, 2026
Make draft model deployment non-interactive Open

Difficulty 2/5 1-3 hours Newbie friendliness 84/100

openvax/mhcflurry#373 · Opened Aug 25, 2026
pyensembl CLI installs wrong genome Open

Difficulty 2/5 1-3 hours Newbie friendliness 70/100

openvax/pyensembl#223 · 5 comments · Opened Jul 30, 2019

openvax

Get new issues in your inbox