Owner

griffithlab

9 indexed repositories · View on GitHub

pVACtools

Python · 188 stars
rnabio.org
website for the rnaseq course

SCSS · 127 stars
civic-v2
CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer

TypeScript · 31 stars
griffithlab.org
Griffith lab research website

JavaScript · 17 stars
civicpy
A python interface for the CIViC db application

Python · 13 stars
civic-docs
Source code for the civicdb.org docs

5 stars
civic-pubtator
Version of tmvar working on ARM with detailed instructions and examples

Shell · 1 star
civic-editor-tools
automations to facilitate editor review and issue correction in civicdb

Python · 0 stars
neoag_vaccine_scripts

Python · 0 stars

Beginner friendly Everything

Open All

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
GKS: Add support for representing evidence star ratings Open

griffithlab/civicpy#256 · 1 assignee · Opened Sep 1, 2026
Capture AI usage attestation Open

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

griffithlab/civic-v2#1498 · Opened Aug 28, 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
Link shortcut to revisions opens to default page Open

enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 64/100

griffithlab/civic-v2#1477 · Opened Aug 19, 2026
Proposal: run CI on pull requests that target feature branches Open

dev-followup

griffithlab/civic-v2#1473 · 1 comment · 1 assignee · Opened Aug 14, 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
GKS: Add support for MPs with cDNA changes in the name Open

Difficulty 3/5 1-2 days Newbie friendliness 38/100

griffithlab/civicpy#255 · 2 comments · Opened Aug 6, 2026
Create GKS Bundle Format for GKS JSON file Open

griffithlab/civicpy#249 · 1 assignee · Opened Aug 3, 2026
Represent FDA Regulatory Approval, FDA Companion Test, and NCCN Guideline using GKS Open

griffithlab/civicpy#244 · 1 assignee · Opened Jul 13, 2026
Consider MinerU as alternative to grobid for publication initial document parsing Open

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

griffithlab/civic-pubtator#1 · Opened Jul 9, 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
GKS: Extension names should use camel case naming convention Open

griffithlab/civicpy#243 · 1 assignee · Opened Jun 30, 2026
Remove the Combined results Open

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

griffithlab/pVACtools#1412 · Opened Jun 29, 2026
Surface citation instructions on help docs and about/help page Open

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

griffithlab/civic-v2#1437 · Opened Jun 26, 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
update `TestCivicGksPredictiveAssertion` once we have an actual approved predictive assertion that is submitted to clinvar Open

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

griffithlab/civicpy#234 · 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
Update R code to tidyverse Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

griffithlab/rnabio.org#102 · Opened May 18, 2026
Clingen API query via gene symbol fails for a few CIViC genes Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

griffithlab/civic-editor-tools#2 · Opened May 1, 2026
Add a reference genome option to `create-vcf` in order to support GRCh38 Open

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

griffithlab/civicpy#222 · Opened Apr 30, 2026
adv. search results table can be pushed offscreen Open

bugfix

griffithlab/civic-v2#1403 · 1 assignee · Opened Apr 29, 2026
Incorrect INFO field encoding in annotate-vcf output, and GRCh38 support for create-vcf Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

griffithlab/civicpy#221 · 2 comments · Opened Apr 29, 2026
Nonsense variants not supported Open

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

griffithlab/civic-editor-tools#1 · Opened Apr 24, 2026
Materialized views should not pre-filter on EID/AID status, deprecation, retraction etc Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

griffithlab/civic-v2#1399 · Opened Apr 23, 2026
Search Examples for Advanced Search Open

enhancement

griffithlab/civic-v2#1398 · 7 comments · 1 assignee · Opened Apr 23, 2026
GKS Exporter: Support Oncogenicity Assertions Open

enhancement

griffithlab/civicpy#217 · 1 comment · 1 assignee · Opened Apr 16, 2026
PubMed scraper improvements/bugfixes Open

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

griffithlab/civic-v2#1391 · Opened Apr 3, 2026
Add ability to clear filter in table views Open

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

griffithlab/civic-v2#1390 · Opened Apr 3, 2026
Hide accept/reject buttons for AIDs and EIDs unless on the summary page Open

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

griffithlab/civic-v2#1386 · Opened Apr 3, 2026
Allow hyperlinks/markdown/html in organization description. Open

Difficulty 2/5 1-3 hours Newbie friendliness 65/100

griffithlab/civic-v2#1385 · Opened Apr 3, 2026
GKS Exporter: Add assembly information to variant Open

griffithlab/civicpy#210 · 2 comments · 1 assignee · Opened Mar 26, 2026
GKS Exporter: Use Cat-VRS and VRS Open

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

griffithlab/civicpy#209 · 4 comments · Opened Mar 26, 2026
Implement automated CIViC AID submissions to ClinVar Open

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

griffithlab/civic-v2#1368 · 3 comments · Opened Mar 19, 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
Support Versioned Sets of Specification Codes Open

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

griffithlab/civic-v2#1348 · Opened Feb 26, 2026
Add instructions for creating and utilizing an API key Open

Difficulty 2/5 1-3 hours Newbie friendliness 25/100

griffithlab/civic-docs#170 · Opened Feb 12, 2026
Strengthen language around medical disclaimers on reuse Open

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

griffithlab/civic-docs#169 · Opened Feb 12, 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
Update HLA comparison script to include HLA-HD Open

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

griffithlab/neoag_vaccine_scripts#43 · Opened Dec 16, 2025
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
Potentially Support Non-Human Genes as Fusion Partners Open

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

griffithlab/civic-v2#1302 · Opened Nov 20, 2025

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