griffithlab/pVACtools

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Stars: 188
Forks: 81
Open beginner issues: 0
Indexed issues: 91
Avg merge: 9d 17h
Merged PRs (30d): 6

Dominant language: Python
License: BSD-3-Clause-Clear
Last GitHub push: Sep 16, 2026
Latest indexed: Sep 20, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed

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91 open issues indexed

Update pVACcompare list of valid columns Open

bug report / hotfix PR

Difficulty 3/5 1-2 days Newbie friendliness 58/100

griffithlab/pVACtools#1465 · Opened Sep 17, 2026
pVACseq should handle frameshift that fall "within the region of the splice site" Open

Difficulty 4/5 3-5 days Newbie friendliness 55/100

griffithlab/pVACtools#1464 · Opened Sep 14, 2026
Don't use special characters in tmp file names Open

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

griffithlab/pVACtools#1455 · Opened Aug 24, 2026
add support for ctat-lr-fusion expression Open

feature addition

griffithlab/pVACtools#1450 · 1 assignee · Opened Aug 11, 2026
Implement a "recommended" algorithm option Open

Difficulty 5/5 Over a week Newbie friendliness 45/100

griffithlab/pVACtools#1449 · Opened Aug 11, 2026
Does pvacseq run support custom HLA/MHC sequencing input via NetMHCpan's -hlaseq option for non-model organisms? Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

griffithlab/pVACtools#1415 · Opened Jul 6, 2026
Consider new stability prediction algorithm SPEARMINT Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

griffithlab/pVACtools#1413 · Opened Jul 1, 2026
Remove the Combined results Open

Difficulty 3/5 1-2 days Newbie friendliness 52/100

griffithlab/pVACtools#1412 · Opened Jun 29, 2026
Add AA -> mRNA backtranslation to pVACvector Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

griffithlab/pVACtools#1411 · Opened Jun 16, 2026
Proposal: staged behavior-preserving refactor of tool responsibility placement Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

griffithlab/pVACtools#1408 · 3 comments · Opened Jun 6, 2026
Update IEDB to use Next-Generation (NG) IEDB Tools API Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

griffithlab/pVACtools#1400 · Opened May 21, 2026
Add NMD prediction support Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

griffithlab/pVACtools#1370 · 1 reaction · Opened Mar 6, 2026
pVACview crashing/blanking out when uploading large metrics.json file (313MB+) Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

griffithlab/pVACtools#1365 · 12 comments · Opened Feb 10, 2026
Suggestion to use WhatsHap for phasing VCFs Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

griffithlab/pVACtools#1362 · 2 comments · 1 reaction · Opened Jan 22, 2026
Investigate AEGIS for class II prediction Open

prediction_algorithms

Difficulty 5/5 Over a week Newbie friendliness 25/100

griffithlab/pVACtools#1361 · Opened Jan 16, 2026
Investigate MARIA for class II predictions Open

prediction_algorithms

Difficulty 5/5 Over a week Newbie friendliness 25/100

griffithlab/pVACtools#1360 · Opened Jan 16, 2026
Use tumor ploidy and cellularity estimates from FACETS and/or Sequenza for clonality assessment Open

feature addition

Difficulty 5/5 Over a week Newbie friendliness 25/100

griffithlab/pVACtools#1355 · 1 comment · Opened Jan 5, 2026
TypeError: a bytes-like object is required, not 'NoneType' Open

bug report / hotfix PR

Difficulty 4/5 3-5 days Newbie friendliness 35/100

griffithlab/pVACtools#1347 · 13 comments · Opened Dec 9, 2025
Investigate adding pMHCchat as an additional binding prediction tool Open

prediction_algorithms

Difficulty 5/5 Over a week Newbie friendliness 25/100

griffithlab/pVACtools#1269 · Opened Jul 15, 2025
Allow filtering and sorting on the Acpt/Rev/Rej columns in pVACview Open

pVACview

Difficulty 3/5 1-2 days Newbie friendliness 20/100

griffithlab/pVACtools#1256 · Opened Jun 25, 2025
Add a command to create a colored ordering TXT/DOC file for DNA vectors Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

griffithlab/pVACtools#1251 · Opened Jun 18, 2025
Running pVACSeq on multiple samples Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

griffithlab/pVACtools#1246 · 13 comments · Opened Jun 3, 2025
Add additional info to pvacsplice aggregate report Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

griffithlab/pVACtools#1239 · 11 comments · Opened May 23, 2025
Incorporate gene of interest status in the aggregate tiering/sorting Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

griffithlab/pVACtools#1230 · Opened Apr 9, 2025
investigate TLimmuno2 Open

prediction_algorithms

Difficulty 5/5 Over a week Newbie friendliness 25/100

griffithlab/pVACtools#1205 · Opened Feb 18, 2025
Console warnings/errors Open

bug report / hotfix PR pVACview

Difficulty 4/5 3-5 days Newbie friendliness 25/100

griffithlab/pVACtools#1199 · Opened Feb 7, 2025
Investigate TLStab (pMHC stability predictor) , TLImm (immunogenicity predictor) Open

prediction_algorithms

Difficulty 5/5 Over a week Newbie friendliness 25/100

griffithlab/pVACtools#1183 · Opened Jan 28, 2025
Consider HLApollo for integration Open

grant prediction_algorithms

Difficulty 5/5 Over a week Newbie friendliness 20/100

griffithlab/pVACtools#1172 · Opened Jan 6, 2025
Plans for adding NetTCR-2.0? Open

prediction_algorithms

Difficulty 5/5 Over a week Newbie friendliness 25/100

griffithlab/pVACtools#1141 · 1 comment · Opened Sep 7, 2024
Potential improvements to the pVACview NeoFox module Open

pVACview

Difficulty 5/5 Over a week Newbie friendliness 20/100

griffithlab/pVACtools#1098 · Opened Apr 30, 2024
Output a visual representation of the graph after all spacers have been tested Open

pVACvector

Difficulty 5/5 Over a week Newbie friendliness 30/100

griffithlab/pVACtools#1089 · 1 comment · Opened Apr 5, 2024
QUESTION: How to integrate netchop results to aditionnally filter possible peptides Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

griffithlab/pVACtools#1064 · Opened Feb 19, 2024
Overview of possible new prediction algorithms and their installation/run requirements Open

prediction_algorithms

Difficulty 4/5 3-5 days Newbie friendliness 35/100

griffithlab/pVACtools#1056 · 2 comments · Opened Jan 26, 2024
Consider integration with ACE a tool for generation of ELISpot configurations (peptide-pool assignments) Open

prediction_algorithms

Difficulty 5/5 Over a week Newbie friendliness 25/100

griffithlab/pVACtools#1051 · Opened Jan 16, 2024
Investigate DeepHLApan prediction algorithm Open

grant prediction_algorithms

Difficulty 5/5 Over a week Newbie friendliness 25/100

griffithlab/pVACtools#1016 · Opened Aug 9, 2023
Evaluate MHCRank for integration Open

prediction_algorithms

Difficulty 5/5 Over a week Newbie friendliness 20/100

griffithlab/pVACtools#1007 · Opened Jul 24, 2023
Add matched WT to pVACfuse predictions Open

grant

Difficulty 5/5 Over a week Newbie friendliness 35/100

griffithlab/pVACtools#993 · Opened Jul 6, 2023
Investigate Pepsickle as an alternative to NetChop Open

prediction_algorithms

Difficulty 4/5 3-5 days Newbie friendliness 25/100

griffithlab/pVACtools#986 · Opened Jun 22, 2023
Update reference proteome analysis to consider patient genotype Open

grant

Difficulty 5/5 Over a week Newbie friendliness 30/100

griffithlab/pVACtools#948 · 3 comments · Opened Apr 7, 2023
Create helper tool that generates information for a peptide order form Open

grant

Difficulty 5/5 Over a week Newbie friendliness 25/100

griffithlab/pVACtools#947 · Opened Apr 5, 2023
Should anchor position be a criteria in the aggregate reprot for class II predictions? Open

grant

Difficulty 5/5 Over a week Newbie friendliness 20/100

griffithlab/pVACtools#940 · 1 comment · Opened Mar 29, 2023
Implement a `--ignore-rna-in-tiering` flag Open

Difficulty 3/5 1-2 days Newbie friendliness 52/100

griffithlab/pVACtools#910 · Opened Mar 6, 2023
Incorporate better handling of HLA allele-specific expression loss Open

grant

Difficulty 5/5 Over a week Newbie friendliness 20/100

griffithlab/pVACtools#901 · Opened Feb 14, 2023
Investigate adding support for EpiScan Predictor Open

grant prediction_algorithms

Difficulty 5/5 Over a week Newbie friendliness 25/100

griffithlab/pVACtools#894 · Opened Jan 9, 2023
Add support for screening of end modifications to long peptides to accommodate manufacture/solubility issues Open

grant

Difficulty 5/5 Over a week Newbie friendliness 25/100

griffithlab/pVACtools#880 · 2 comments · Opened Dec 6, 2022
Implement a tool/step that identifies peptides that could be toxic Open

grant prediction_algorithms

Difficulty 5/5 Over a week Newbie friendliness 25/100

griffithlab/pVACtools#863 · 4 comments · Opened Nov 2, 2022
Add retry when NetMHCstabpan fails Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

griffithlab/pVACtools#862 · Opened Oct 27, 2022
Explore incorporation of "Inhibigens" in neoantigen candidate prioritization Open

grant

Difficulty 5/5 Over a week Newbie friendliness 25/100

griffithlab/pVACtools#829 · 2 comments · Opened Jul 14, 2022
Use MHCgnomes to help resolve HLA alleles Open

grant

Difficulty 5/5 Over a week Newbie friendliness 25/100

griffithlab/pVACtools#827 · Opened Jul 11, 2022
pVACseq stability predictions are not performed locally with --netmhc-stab Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

griffithlab/pVACtools#791 · 1 comment · Opened Apr 4, 2022

griffithlab/pVACtools

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