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griffithlab
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pVACtools
http://www.pvactools.org
BSD 3-Clause Clear License
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Update pVACview documentation (vignette) and pVACview Tutorials page to mention anchor weights and anchor distribution tables
#1140
susannasiebert
opened
1 day ago
0
Fix issue where class ii alleles were filtered out as invalid before combining alpha and beta chains
#1139
susannasiebert
closed
10 hours ago
0
The .aggregated.metrics.json file is not always generated
#1138
lukaas33
opened
1 week ago
3
pVACview updates for paper review
#1137
susannasiebert
closed
9 hours ago
0
Bump setuptools from 57.4.0 to 70.0.0 in /docs
#1136
dependabot[bot]
closed
2 weeks ago
1
Add test for proximal variant file generation
#1135
susannasiebert
closed
2 weeks ago
0
Allow aggregated TSV as an input to pvacfuse generate_protein_fasta command
#1134
susannasiebert
closed
2 weeks ago
0
Remove some alleles from MHCnuggets
#1133
susannasiebert
closed
2 weeks ago
0
Add funding page
#1132
susannasiebert
closed
2 weeks ago
0
Add support for dog alleles for NetMHCpan
#1131
susannasiebert
opened
3 weeks ago
1
Handle invalid pVACfuse characters by trimming sequence
#1130
susannasiebert
closed
2 weeks ago
0
Add page for pVACtools courses
#1129
susannasiebert
closed
2 weeks ago
0
pVACview: neofox_ui.R and custom_ui.R not found in the output folder
#1128
LukaszGraff
closed
2 weeks ago
2
CannotConvertValueError for vcf file
#1127
lukaas33
closed
3 weeks ago
2
Add new pVACview R files to the list of files getting copied into the pVACseq output folder
#1126
susannasiebert
closed
2 weeks ago
0
pVACFuse: KeyError: '25.GCN1-MSI1.ENST00000300648.7-ENST00000257552.7.inframe_fusion.32'
#1125
MaxMichaeler
closed
2 weeks ago
1
KeyError: 'mhcflurry_processing_score'
#1123
hangfafa
closed
1 month ago
5
Remove unused code in the Frameshift.pm VEP plugin
#1122
susannasiebert
closed
1 month ago
0
Skip variants where VEP didn't predict an amino acid change
#1121
susannasiebert
closed
1 month ago
0
CannotConvertValue: 125,142 cannot be converted to Integer, keeping as string
#1120
dincerkilic
closed
1 month ago
2
BigMHC prediction not working
#1119
giacuong171
closed
2 months ago
3
pVACseq: Discrepancy between {sample_id}.all_epitopes.tsv and {sample_id}.fasta ?
#1118
yiolino
opened
2 months ago
6
Updated mouse anchor data links
#1117
ldhtnp
closed
2 weeks ago
0
fixing rounding issue in min-max slider
#1116
evelyn-schmidt
closed
1 month ago
2
Only check for refseq_select_prot blast db species compatibility if ref proteome similarity step is run with blast
#1115
susannasiebert
closed
2 months ago
0
Output anchor positions currently applied to the data in pVACview
#1114
susannasiebert
closed
2 weeks ago
0
Issue/1109 Minor pVACview improvements
#1113
ldhtnp
closed
2 months ago
0
Method for decomposing MT-WT aa sequences
#1112
nttvy
closed
1 month ago
4
NetChop SSLError
#1111
Tseng722
closed
2 months ago
1
Added support for mouse specific allele anchor positions
#1110
ldhtnp
closed
2 months ago
1
Minor pVACview improvements
#1109
susannasiebert
closed
2 months ago
0
Added new valid_algorithms command (#1106)
#1108
ldhtnp
closed
3 months ago
0
Frameshift VEP plugin
#1107
SirKuikka
closed
2 weeks ago
6
Implement new command `pvacseq valid_algorithms` to see which prediction algorithms support a specific allele and/or species
#1106
susannasiebert
closed
2 months ago
0
Add an option to the valid_alleles command(s) to filter output by species
#1105
susannasiebert
closed
3 months ago
0
Zero or few results after filtering
#1104
SirKuikka
closed
3 weeks ago
6
Support for custom epitope prediction algorithms
#1103
boyangzhao
closed
3 weeks ago
2
help with pVACseq customization
#1101
javierAPC
closed
3 months ago
2
Reviewing PR #1062
#1100
susannasiebert
closed
4 months ago
0
if protein_identifiers_from_label[protein_label] is not None: KeyError: 92
#1099
brycemash
closed
4 months ago
2
Potential improvements to the pVACview NeoFox module
#1098
susannasiebert
opened
4 months ago
0
Update pvacseq_vignette.rst
#1097
chrisamiller
closed
3 months ago
1
Update pvacseq_upload.rst
#1096
chrisamiller
closed
4 months ago
1
Update pvacseq_features.rst
#1095
chrisamiller
closed
4 months ago
1
Fix incorrect transcript2 parsing from Arriba
#1094
susannasiebert
closed
4 months ago
0
Consider integration of MixMHCPred2
#1093
malachig
opened
4 months ago
1
Version of tools used in pVacFuse
#1092
min-codes
closed
3 months ago
2
Generate protein fasta prox vars
#1091
evelyn-schmidt
closed
3 months ago
0
Prefilter pVACseq and pVACsplice on a user-defined list of biotypes
#1090
susannasiebert
opened
5 months ago
0
Output a visual representation of the graph after all spacers have been tested
#1089
susannasiebert
opened
5 months ago
0
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