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andrewrech
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antigen.garnish
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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
implement GNU parallels over netMHC threads
#109
leeprichman
closed
4 years ago
3
BLAST db not found
#108
leeprichman
closed
5 years ago
1
Upgrade netMHCpan support to 4.0
#107
leeprichman
closed
5 years ago
1
Add sanity check for reference allele for direct cDNA_change transcript level input
#106
leeprichman
closed
5 years ago
1
garnish_slim()
#105
ghost
closed
6 years ago
0
antigen.garnish #458 failed
#104
andrewrech
closed
6 years ago
0
remove biomaRt dependencies
#103
leeprichman
closed
6 years ago
1
Reduce collate_netMHC memory usage
#102
leeprichman
closed
5 years ago
1
Add additional tools to workflow
#101
leeprichman
closed
5 years ago
1
hg19 annotations from snpeff give refseq ids
#100
leeprichman
closed
6 years ago
1
example vcfs not available?
#99
ghost
closed
5 years ago
19
Clone wars ajr late
#98
andrewrech
closed
6 years ago
2
correct tests in AJR clonality branch
#97
andrewrech
closed
6 years ago
0
confirm correctness of garnish_clonality calculations after upstream changes
#96
andrewrech
closed
6 years ago
1
Upload new .tar.gz release to Github
#95
andrewrech
closed
5 years ago
2
Detailed analysis vignette
#94
leeprichman
closed
5 years ago
3
Match VCFs and clonality tables on file names
#93
leeprichman
closed
6 years ago
0
simplifying neoepitope output data table
#92
andrewrech
closed
5 years ago
1
specify input data table to clonality function
#91
andrewrech
closed
6 years ago
2
add detailed svg to wiki
#90
andrewrech
closed
6 years ago
3
Merge clonality branch
#89
leeprichman
closed
6 years ago
8
getting even with master
#88
leeprichman
closed
6 years ago
0
Add tests for mutect1 input +/- cell fraction info
#87
leeprichman
closed
6 years ago
1
No check for non-standard AA's in input to garnish_predictions
#86
leeprichman
closed
6 years ago
1
Accept MuTect2 VCFs with clonality estimation as standard input
#85
andrewrech
closed
6 years ago
3
Addition of Wiki
#84
ghost
closed
6 years ago
2
garnish_fitness is not returning `R` or `A`
#83
ghost
closed
6 years ago
7
error with README.md example
#82
ghost
closed
6 years ago
8
Update garnish
#81
leeprichman
closed
6 years ago
1
Whitelist blastp results
#80
leeprichman
closed
6 years ago
0
List licensing requirements of dependencies in README
#79
andrewrech
closed
6 years ago
3
Document blast flags
#78
andrewrech
closed
6 years ago
0
Remove hard-coded path dependencies to data directory
#77
andrewrech
closed
6 years ago
0
Edge case fixes, R implementation of fitness model
#76
leeprichman
closed
6 years ago
6
Update antigen.garnish_predict.R
#75
leeprichman
closed
6 years ago
0
Make CLI
#74
andrewrech
closed
6 years ago
1
Error when vcfs do not contain bam file names in header as in VarScan
#73
leeprichman
closed
6 years ago
1
Adapt python scripts to run fitness on all nmer
#72
leeprichman
closed
6 years ago
1
garnish_fitness returns fitness scores averaged across all class I alleles
#71
leeprichman
closed
6 years ago
1
bug fix for edge case in garnish_predictions
#70
leeprichman
closed
6 years ago
0
Updates to garnish_summary and _plot
#69
leeprichman
closed
6 years ago
1
Get even with master before merge
#68
leeprichman
closed
6 years ago
0
Update plot function for fitness calculations
#67
andrewrech
closed
6 years ago
1
Make web API
#66
andrewrech
closed
6 years ago
1
JAFFA gene names != mgi_symbol from biomaRt
#65
andrewrech
closed
6 years ago
2
Make Docker image
#64
andrewrech
closed
6 years ago
1
BiomaRt not working with Ensembl 91
#63
andrewrech
closed
6 years ago
1
Garnish_fitness update
#62
leeprichman
closed
6 years ago
0
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