griffithlab pVACtools issues

griffithlab / pVACtools

http://www.pvactools.org

BSD 3-Clause Clear License

144 stars 59 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Adding Gene and Transcript Expression to VCF for pVACseq

#1159 biounix opened 1 day ago
6
Error: No command specified

#1158 Geneece opened 2 days ago
1
Error

#1157 Geneece closed 2 days ago
0
Add additional trailing amino acids for frameshift insertions when creating fasta

#1155 susannasiebert opened 1 month ago
0
[Bug report title]NoneType Error Encountered with NetMHCpan and Exception When Calling MHCflurry

#1154 anomibo closed 1 month ago
3
Fix bug where the incorrect neoantigen fasta entry was used for ref proteome search

#1153 susannasiebert opened 1 month ago
0
Help with MT-WT epitope match for inframe mutations

#1152 KhacDuyNguyen0 opened 1 month ago
4
BigMHC and DeepImmuno future support

#1151 Stikus closed 1 month ago
5
`ValueError: substring not found` when running proteome similarity search with pvacseq

#1150 lukaas33 opened 2 months ago
2
Update pVACview percentile plots to include percentiles from elution and immunogenicity algorithms

#1149 susannasiebert opened 2 months ago
0
Add new alleles that weren't previously supported

#1148 susannasiebert opened 2 months ago
0
Fix aggregate inclusion binding threshold and add new --aggregate-inclusion-count-limit parameter

#1147 susannasiebert opened 2 months ago
1
MHC allele supported by the original prediction method, but not recognized by pvacseq

#1146 luyh-xp opened 2 months ago
3
Update class II pVACview demo data to match updated allele handling

#1145 susannasiebert closed 2 months ago
0
Update pVACview anchor figure

#1144 susannasiebert closed 2 months ago
0
Don't write extra title line to excel export spreadsheets

#1143 susannasiebert closed 2 months ago
0
Allow passing candidates to be based on binding OR percentile cutoff.

#1142 malachig opened 2 months ago
2
Plans for adding NetTCR-2.0?

#1141 lukaas33 opened 2 months ago
1
Update pVACview documentation (vignette) and pVACview Tutorials page to mention anchor weights and anchor distribution tables

#1140 susannasiebert opened 2 months ago
0
Fix issue where class ii alleles were filtered out as invalid before combining alpha and beta chains

#1139 susannasiebert closed 2 months ago
0
The .aggregated.metrics.json file is not always generated

#1138 lukaas33 opened 2 months ago
3
pVACview updates for paper review

#1137 susannasiebert closed 2 months ago
0
Bump setuptools from 57.4.0 to 70.0.0 in /docs

#1136 dependabot[bot] closed 3 months ago
1
Add test for proximal variant file generation

#1135 susannasiebert closed 3 months ago
0
Allow aggregated TSV as an input to pvacfuse generate_protein_fasta command

#1134 susannasiebert closed 3 months ago
0
Remove some alleles from MHCnuggets

#1133 susannasiebert closed 3 months ago
0
Add funding page

#1132 susannasiebert closed 3 months ago
0
Add support for dog alleles for NetMHCpan

#1131 susannasiebert opened 3 months ago
1
Handle invalid pVACfuse characters by trimming sequence

#1130 susannasiebert closed 3 months ago
0
Add page for pVACtools courses

#1129 susannasiebert closed 3 months ago
0
pVACview: neofox_ui.R and custom_ui.R not found in the output folder

#1128 LukaszGraff closed 3 months ago
2
CannotConvertValueError for vcf file

#1127 lukaas33 closed 3 months ago
2
Add new pVACview R files to the list of files getting copied into the pVACseq output folder

#1126 susannasiebert closed 3 months ago
0
pVACFuse: KeyError: '25.GCN1-MSI1.ENST00000300648.7-ENST00000257552.7.inframe_fusion.32'

#1125 MaxMichaeler closed 3 months ago
1
KeyError: 'mhcflurry_processing_score'

#1123 hangfafa closed 4 months ago
5
Remove unused code in the Frameshift.pm VEP plugin

#1122 susannasiebert closed 4 months ago
0
Skip variants where VEP didn't predict an amino acid change

#1121 susannasiebert closed 4 months ago
0
CannotConvertValue: 125,142 cannot be converted to Integer, keeping as string

#1120 dincerkilic closed 4 months ago
2
BigMHC prediction not working

#1119 giacuong171 closed 4 months ago
3
pVACseq: Discrepancy between {sample_id}.all_epitopes.tsv and {sample_id}.fasta ?

#1118 yiolino opened 4 months ago
6
Updated mouse anchor data links

#1117 ldhtnp closed 3 months ago
0
fixing rounding issue in min-max slider

#1116 evelyn-schmidt closed 4 months ago
2
Only check for refseq_select_prot blast db species compatibility if ref proteome similarity step is run with blast

#1115 susannasiebert closed 5 months ago
0
Output anchor positions currently applied to the data in pVACview

#1114 susannasiebert closed 3 months ago
0
Issue/1109 Minor pVACview improvements

#1113 ldhtnp closed 5 months ago
0
Method for decomposing MT-WT aa sequences

#1112 nttvy closed 4 months ago
4
NetChop SSLError

#1111 Tseng722 closed 5 months ago
1
Added support for mouse specific allele anchor positions

#1110 ldhtnp closed 5 months ago
1
Minor pVACview improvements

#1109 susannasiebert closed 5 months ago
0
Added new valid_algorithms command (#1106)

#1108 ldhtnp closed 5 months ago
0