HLAminer statistics

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Associated diseases

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HLAminer specifications

Information


Unique identifier OMICS_06137
Name HLAminer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for HLAminer

HLAminer in publications

 (6)
PMCID: 5834780
PMID: 29288513
DOI: 10.1111/cas.13498

[…] been developed to obtain hla allele information from genome‐wide sequencing data (whole‐exome, whole‐genome, and rna sequencing data), including optitype, polysolver, phlat, hlareporter, hlaforest, hlaminer, and seq2hla. we have tested 961 whole‐exome data from the 1000 genomes project to evaluate the accuracy of these programs. among these algorithms, optitype showed the highest accuracy […]

PMCID: 5814272
PMID: 29487705
DOI: 10.18632/oncotarget.23742

[…] all genes with available tcga data from the gene ontology (go) accession number 0060337 [, ]., hla typing, neo-antigen identification, and hla-peptide affinity prediction were performed using hlaminer [], variant effect predictor tool [], netmhcpan [], and the ucsc browser [] (http://www.genome.ucsc.edu/), with most computations performed on the national cancer institute (nci) cancer […]

PMCID: 5662567
PMID: 29084941
DOI: 10.1038/s41467-017-01178-z

[…] data were clustered using a drichlet process, estimating the number of mutation-defined clusters/tumor., neoepitopes resulting from gene fusions were integrated with predicted hla alleles from hlaminer by integrate-neo. for both fusion genes and mutations, netmhc 4.0 was used for neoantigen-binding prediction., sections (5 μm) of ffpe tumor tissue were stained with antibodies specific […]

PMCID: 4951244
PMID: 26871478
DOI: 10.18632/oncotarget.7293

[…] size, we have not a direct evidence that the mutated proteins generate neoantigens, but have used instead bioinformatics prediction tools. moreover, it has been reported that hla inference program hlaminer achieves a good performance with rna-seq or whole genome data rather than with exome sequencing data []. finally, it is well known that each gene could codify several protein isoforms. […]

PMCID: 4660052
PMID: 26311539
DOI: 10.1038/jhg.2015.102

[…] rates compared with those of the existing pcr-sso or pcr-sequencing-based typing results., as described in , various hla-typing software programs, including the aforementioned omixon target hla and hlaminer, as well as academic software and commercial software packages, have been developed for hla typing from various types of data, including wgs, wes, rna sequencing and amplicon datasets., , , […]


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HLAminer institution(s)
BC Cancer Agency, Michael Smith Genome Sciences Centre, Vancouver, BC, Canada

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