openvax vaxrank issues - Githubissues

openvax / vaxrank

Ranked vaccine peptides for personalized cancer immunotherapy

Apache License 2.0

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Add more predictions to EpitopePrediction

#201 iskandr opened 2 months ago
0
Make Vaxrank's epitope/vaccine peptide scoring/filtering/ranking more configurable via YAML

#200 iskandr opened 2 months ago
1
Make scoring, filtering, and ranking rules configurable

#199 iskandr opened 3 months ago
0
added dev scripts

#198 iskandr closed 5 months ago
0
Build issues with jinja2.ext

#197 saraahwallace opened 11 months ago
1
Fix running vaxrank

#196 Emon46 closed 1 year ago
1
update cutoff with el_score

#195 Emon46 closed 1 year ago
0
Peg jinja2 version

#194 timodonnell closed 1 year ago
0
ValueError: Invalid contig name 'chr14_GL000194v1_random' for reference 'GRCh38'

#193 leldershaw opened 3 years ago
2
ValueError: Unable to infer reference genome

#192 Shuhui-d opened 3 years ago
1
Use Isovar for all variant counts, change Python versions in tests to 3.6 and 3.7

#191 iskandr closed 3 years ago
1
Last bits of making Vaxrank work with new Isovar

#190 julia326 closed 3 years ago
0
Vaxrank '--output-neoepitope-report' fails on StopLoss variants

#189 JPFinnigan opened 4 years ago
0
Add N-terminal methionine check to manufacturability

#188 julia326 opened 4 years ago
1
A way from VCF format to mutated peptides only

#187 nishuai closed 4 years ago
2
use new Isovar API but keep old logic for determining variant effects

#186 iskandr closed 4 years ago
1
Split VaxrankCoreLogic into smaller stateless functions

#185 iskandr closed 4 years ago
1
Removed namedtuple, other small changes in preparation for rewrite

#184 iskandr closed 4 years ago
1
Use faster k-mer index for proteome instead of full FM index

#183 iskandr opened 4 years ago
0
Change all namedtuples to Serializable

#182 iskandr closed 4 years ago
1
Rename "epitope" to "MHC ligand"

#181 iskandr opened 4 years ago
0
Use new Isovar API

#180 iskandr closed 4 years ago
1
Soften the requirements of vaxrank for isovar version

#179 golubnikova opened 4 years ago
1
Errors when writing XLSX file

#178 code12412f opened 5 years ago
6
broader version range for isovar, still excluding newest isovar PR

#177 iskandr closed 5 years ago
0
Don't use the new Isovar version when it's merged

#176 iskandr closed 5 years ago
2
Add --download-reference-genome-data arg to Vaxrank test run script.

#175 julia326 closed 5 years ago
1
Add low priority vaccine peptide filtering for C terminal residues that cause racemization

#174 iskandr opened 5 years ago
0
Update paper

#173 iskandr closed 5 years ago
0
Superficial cleanup

#172 iskandr closed 5 years ago
1
Don't want to minimize GRAVY score

#171 iskandr opened 5 years ago
0
Showing 5 significant figures for floats in Vaxrank reports.

#170 julia326 closed 5 years ago
1
Fixing how we package data/* files.

#169 julia326 closed 5 years ago
1
Keep all variants, add gene set membership check

#168 julia326 closed 5 years ago
2
How many variant callers can be used with vaxrank?

#167 davidroberson closed 6 years ago
1
Get genome in unit tests without forcing specific Ensembl release version

#166 iskandr closed 6 years ago
0
Add class II predictions to report

#165 julia326 opened 6 years ago
0
Vaxrank with netmhcpan-iedb errors on IDH1 test data

#164 julia326 opened 6 years ago
0
Fix isovar import

#163 iskandr closed 6 years ago
1
Using an environment variable to set where the reference peptide index lives.

#162 julia326 closed 6 years ago
2
Making --max-mutations-in-report an output arg.

#161 julia326 closed 6 years ago
0
Fixing serialization of VaccinePeptide objects

#160 julia326 closed 6 years ago
1
Creating a report from JSON is broken

#159 julia326 closed 6 years ago
0
Adding IGV locus to the ASCII/PDF vaxrank report templates.

#158 julia326 closed 6 years ago
2
Fix pypi autodeploy

#157 julia326 closed 6 years ago
0
Include gene name in Excel output

#156 iskandr opened 6 years ago
1
Add option to exclude variants from JPT report

#155 julia326 opened 6 years ago
0
Add tissue expression to each variant

#154 iskandr opened 6 years ago
0
Add gene summary to each variant

#153 iskandr opened 6 years ago
1
Computing some counts for the vaxrank report in the core logic

#152 julia326 closed 6 years ago
0