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andrewrech
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antigen.garnish
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Skipping BLAST because ncbiblast+ is not in PATH
#159
guanghua13
opened
6 months ago
0
netMHCII: not found
#158
GHosking-01
opened
8 months ago
0
Illegal argument in garnish_variants
#157
saharlccSCSU
opened
8 months ago
0
Antigen.garnish missing columns in output file with fusion peptides
#156
GHosking-01
opened
9 months ago
4
Foreignness for mouse data
#155
saraahwallace
opened
10 months ago
2
no score calculated
#154
dxl3742
closed
1 year ago
3
Question about neoantigen abundance (TPM) from "Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction"
#153
zhaoxiaofei
closed
1 year ago
1
dai_uuid output column
#152
SofiaOtero
closed
10 months ago
3
Antigen Garnish output and Expression file
#151
SofiaOtero
closed
2 years ago
21
Understanding garnish_antigens output table
#150
antaralabiba97
closed
10 months ago
1
garnish_affinity process killed when running all human alleles
#149
antaralabiba97
closed
2 years ago
3
Running netMHC
#148
SofiaOtero
opened
2 years ago
31
Using own vcf file in docker
#147
antaralabiba97
closed
2 years ago
2
No outputs for some queries when estimating foreignness scores
#146
ARChakravarthy
closed
2 years ago
2
Update tutorial to 2.3
#145
itamuria
closed
2 years ago
1
garnish_antigens filtering
#144
nickhir
closed
2 years ago
2
Nomenclature MHC II
#143
nickhir
closed
2 years ago
1
Unable to download netMHC data tar from DTU.
#142
nickhir
closed
2 years ago
11
garnish_affinity ; data.table error, function breaks after it starts extracting cDNA changes
#141
ARChakravarthy
closed
3 years ago
13
Error: unset environmental variable for antigen.garnish data directory
#140
ARChakravarthy
closed
3 years ago
5
Backwards compatibility with hg19
#139
ARChakravarthy
closed
3 years ago
1
running just foreignness leads to warnings/errors
#138
boyangzhao
closed
3 years ago
10
Docker update
#137
andrewrech
closed
3 years ago
6
Enhanced Documentation. GRCh37 reference genome.
#136
nickhir
closed
3 years ago
7
Process Killed
#135
itamuria
closed
3 years ago
2
Allow setting threads using environment variable; fix test for refseq support; fix ensemble score edge case
#134
andrewrech
closed
3 years ago
0
The applicability of this software
#133
MaryGoAround
closed
3 years ago
12
Running your software via docker
#132
beginner984
closed
3 years ago
67
2.0
#131
andrewrech
closed
3 years ago
0
Update ensemsbl annot
#130
andrewrech
closed
3 years ago
0
Dev
#129
andrewrech
closed
3 years ago
0
Update ensemsbl annot
#128
andrewrech
closed
3 years ago
0
Readme fix
#127
andrewrech
closed
3 years ago
0
Specify that GRChm38_meta.RDS file in antigen.garnish data directory …
#126
andrewrech
closed
3 years ago
1
Readme fix, begin migration to Ensembl only
#125
andrewrech
closed
3 years ago
0
'v %>% data.table::as.data.table' pipe syntax fails in recent R-- parentheses required for namespace-prefixed functions
#124
danoreper
closed
4 years ago
6
Error with class II
#123
itamuria
closed
4 years ago
3
Why is it downloading each time?
#122
itamuria
closed
4 years ago
2
netMHC data lose ?
#121
BioLaoXu
closed
4 years ago
2
mkdir: cannot create directory ‘/scratch’: Permission denied
#120
itamuria
closed
4 years ago
2
garnish_affinity fails when specify mut, wt peptide and index
#119
ShixiangWang
closed
4 years ago
4
Update README.md
#118
andrewrech
closed
4 years ago
0
Origin/new config
#117
leeprichman
closed
4 years ago
1
mhcflurry-predict is not in PATH
#116
itamuria
closed
4 years ago
7
magrittr version issue with antigen.garnish/1.1.0
#115
ShahiRB
closed
4 years ago
3
Config of netMHC may lead to error in `garnish_affinity()`
#114
SilenWang
closed
4 years ago
4
Peptide level
#113
leeprichman
closed
4 years ago
0
`system()` can't work correctly after running the demo in document
#112
SilenWang
closed
4 years ago
3
Fix bug with "all" MHC option
#111
leeprichman
closed
4 years ago
0
Error when running example in document
#110
SilenWang
closed
4 years ago
4
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