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openvax
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topiary
Predict mutated T-cell epitopes from sequencing data
Apache License 2.0
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ValueError: Invalid contig name 'chr1' for reference 'GRCh38
#89
pswetha
opened
2 years ago
0
The meaning of contains_mutant_residues
#88
ysbioinfo
opened
5 years ago
0
Request for inclusion of wild-type peptide binding affinity
#87
ARChakravarthy
opened
5 years ago
0
Permission denied or got an unexpected keyword argument 'models_path'
#86
GSDenghj
closed
6 years ago
2
add --protein-change commandline arg
#85
iskandr
closed
6 years ago
0
Refactor for protein sequences
#84
iskandr
closed
6 years ago
1
Move to OpenVax organization
#83
tavinathanson
closed
6 years ago
1
Namedtuples -> Objects
#82
iskandr
closed
6 years ago
2
TopiaryPredictor
#81
iskandr
closed
6 years ago
2
Request for Abbreviated HTML parameter/output
#80
mikekubal
opened
6 years ago
0
BLAST epitopes against reference proteome
#79
iskandr
opened
6 years ago
1
Get rid of "wildtype ligandome" dictionary
#78
iskandr
opened
6 years ago
0
Issue locating NetMHCpan
#77
ARChakravarthy
closed
6 years ago
1
reorganizing commandline interface to resemble mhctools and other hammerlab Python tools
#76
iskandr
closed
6 years ago
5
Error in running topiary
#75
bbhinder
opened
6 years ago
0
Error: missing binding predictions
#74
kevin199011
opened
6 years ago
4
Adding a short RELEASING.md
#73
julia326
closed
7 years ago
1
Upping mhctools dependency version, also topiary version for release.
#72
julia326
closed
7 years ago
2
Add a RELEASING.md
#71
julia326
closed
7 years ago
1
ValueError: Expected 484916 peptide predictions but got 267878
#70
ihodes
opened
7 years ago
1
Topiary import error
#69
ihodes
closed
7 years ago
1
Grant owner access to hammerlab on pypi
#68
armish
closed
7 years ago
2
Import normalize_allele_name from mhcnames instead mhctools
#67
armish
closed
7 years ago
4
Updated to work with mhctools 1.0.0
#66
iskandr
closed
7 years ago
1
Cannot run Topairy on my dataset.
#65
Akado2009
opened
7 years ago
4
Fixing test after netMHCpan 2.8 -> 3.0 update.
#64
julia326
closed
7 years ago
1
Test failing after netMHCpan update
#63
julia326
closed
7 years ago
0
Optionally use isovar to construct coding/protein sequence
#62
iskandr
opened
7 years ago
4
self-ligandome filter fails when unusual alleles have epitopes
#61
kippakers
closed
7 years ago
1
Removed argparsing code for pMHC prediction and variant loading
#60
iskandr
closed
8 years ago
2
'Namespace' object has no attribute 'rna_gene_fpkm_file'
#59
cedarice
closed
7 years ago
2
Wildtype peptide sequence
#58
iskandr
opened
8 years ago
0
Cleaned up commandline arguments
#57
iskandr
closed
8 years ago
5
VCF annotation
#56
serge2016
opened
8 years ago
9
Question: How are frameshifts handled?
#55
kippakers
closed
8 years ago
2
Trim protein sequences to not include stop codons
#54
iskandr
closed
8 years ago
1
Peptides with * in sequence causing trouble (with netMHCcons)
#53
kippakers
closed
8 years ago
8
Make sure we'll correctly translating chr13 g.5864876_5864877insG (mm10)
#52
iskandr
closed
8 years ago
4
Error of unknown origin
#51
kippakers
closed
8 years ago
9
Add __version__
#50
tavinathanson
closed
8 years ago
4
Replace "self-ligandome" filtering with just search over the full proteome
#49
iskandr
opened
8 years ago
5
Don't seem to be filtering stop-gain variants
#48
iskandr
opened
8 years ago
4
NCBIM37
#47
gmicevic
closed
8 years ago
4
Update README.md
#46
tavinathanson
closed
8 years ago
2
Clarify what NetMHC* versions are supported
#45
tavinathanson
opened
8 years ago
0
Change default NetMHC implementation to NetMHC4 in mhctools
#44
iskandr
closed
8 years ago
1
Needs a DOI for citations
#43
iskandr
closed
8 years ago
0
Invalid percentile rank epitopes
#42
rschenck
opened
8 years ago
5
Topiary w/ NetMHC Fails
#41
JPFinnigan
opened
8 years ago
13
Added option to read transcript FPKM values from StringTie GTF file
#40
iskandr
closed
8 years ago
4
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