ImmCancer: Cancer Immunotherapy Knowledgebase

Welcome to HLA-Based Tools Page of ImmCancer

On this page, we have enlisted insilico tools/pipelines for HLA-typing, which may be further used for designing cancer immunotherapy. The given table comprises genome profile repositories. The first column represents the Name of the database, and the rest of the columns represents the Year, Description, Reference, and working status of the database. Click on the headers to sort them accordingly.

Name	Year	Description	Functional
seq2HLA	2012	A computational tool to determine HLA (Class I and II) from short RNA-Seq reads	YES
HLAminer	2012	Derivation of class I HLA predictions from shotgun sequence datasets	YES
ATHLATES	2013	Accurate typing of class I HLA through whole exome sequencing	YES
HLAforest	2013	Class I and II HLA typing using RNA-seq data	YES
OptiType	2014	Class I HLA genotyping from NGS data using integer linear programming algorithm	YES
HLAreporter	2015	Class I and II HLA typing from NGS data based on read-mapping using a comprehensive reference panel.	YES
HLA-VBSeq	2015	Full resolution (8-digit) class I HLA typing using WGS data	YES
Polysolver	2016	high precision HLA-typing even while using relatively low coverage WES data, and a subsequent mutation detection pipeline that uses the inferred alleles as a basis for high fidelity detection of mutations in HLA genes	YES
xHLA	2017	Fast and accurate HLA typing (Class I & II) from short-read next-generation sequence data with xHLA	YES
HLA-HD	2017	An accurate HLA typing (Class I & II) algorithm for next-generation sequencing data	YES
PHLAT	2018	Inference of High-Resolution HLA types (Class I & II) from RNA-Seq and WES data	YES
STC-Seq	2018	High-sensitivity HLA typing (Class I & II) by Saturated Tiling Capture Sequencing	YES
Kourami	2018	Graph-guided assembly for (Class I & II)novel HLA allele discovery using WGS data	YES
HLA*LA	2019	Class I and II HLA typing from linearly projected graph alignments using WGS, WES data	YES
HLA-IMPUTER	2019	Implements the HIBAG algorithm for HLA class I & II allele imputation using SNP genotypes	YES
HLA-VBSeq v2	2019	Class I & II HLA calling tool from high-throughput sequencing data	YES
HISAT-genotype	2020	Supports HLA typing, the discovery of novel HLA alleles using WGS data	YES
SOAPTyping	2020	Sequence-based typing for HLA class I and II alleles from RNA-seq data	YES
HLAssign 2.0	2020	Graphical User Interface for the analysis of short and long read Human Leukocyte Antigen-typing data	YES
HLArestrictor	2011	Patient-Speci fi c HLA Restriction Elements and Optimal Epitopes Within Peptides	YES
HLA-CNN	2017	HLA class I binding prediction via convolutional neural networks	YES
HLAthena	2020	Allele-and-length-specific and pan-allele-pan-length prediction models for endogenous peptide presentation.	YES
scHLAcount	2020	Allele-specific HLA expression from single-cell gene expression data	YES
HLA-DR4Pred	2004	Prediction of MHC Class II alleles (HLA-DRB1*0401) binding peptides.	YES
nHLAPred	2007	Prediction of MHC Class I binders	YES
Hlaffy	2016	Estimates affinities of peptide for Class I MHC molecules	NO
ProPred	2001	Prediction of HLA-DR binders.	YES
ProPred1	2003	Prediction of MHC-I binders	YES