andrewrech antigen.garnish issues

andrewrech / antigen.garnish

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issues

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Running the code given by developer as an example generates the error!

#162 Xiao-Zhong opened 1 week ago
5
Read my VCF file with an error.

#161 Xiao-Zhong opened 1 month ago
1
Error in library(rio) : there is no package called ‘rio’

#160 gr125 opened 3 months ago
0
Skipping BLAST because ncbiblast+ is not in PATH

#159 guanghua13 closed 1 week ago
4
netMHCII: not found

#158 GHosking-01 closed 3 months ago
0
Illegal argument in garnish_variants

#157 saharlccSCSU closed 3 months ago
0
Antigen.garnish missing columns in output file with fusion peptides

#156 GHosking-01 closed 3 months ago
4
Foreignness for mouse data

#155 saraahwallace closed 3 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 1 year ago
3
Antigen Garnish output and Expression file

#151 SofiaOtero closed 2 years ago
21
Understanding garnish_antigens output table

#150 antaralabiba97 closed 1 year ago
1
garnish_affinity process killed when running all human alleles

#149 antaralabiba97 closed 2 years ago
3
Running netMHC

#148 SofiaOtero closed 3 months 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 3 years ago
1
Unable to download netMHC data tar from DTU.

#142 nickhir closed 3 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 4 years ago
2
Allow setting threads using environment variable; fix test for refseq support; fix ensemble score edge case

#134 andrewrech closed 4 years ago
0
The applicability of this software

#133 MaryGoAround closed 4 years ago
12
Running your software via docker

#132 beginner984 closed 3 years ago
67
2.0

#131 andrewrech closed 4 years ago
0
Update ensemsbl annot

#130 andrewrech closed 4 years ago
0
Dev

#129 andrewrech closed 4 years ago
0
Update ensemsbl annot

#128 andrewrech closed 4 years ago
0
Readme fix

#127 andrewrech closed 4 years ago
0
Specify that GRChm38_meta.RDS file in antigen.garnish data directory …

#126 andrewrech closed 4 years ago
1
Readme fix, begin migration to Ensembl only

#125 andrewrech closed 4 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 5 years ago
3
Config of netMHC may lead to error in `garnish_affinity()`

#114 SilenWang closed 5 years ago
4
Peptide level

#113 leeprichman closed 5 years ago
0