In-silico method written in Python and R to determine HLA genotypes of a sample. seq2HLA takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising all HLA alleles and outputs the most likely HLA class I and class II genotypes (in 4 digit resolution), a p-value for each call, and the expression of each class.
☆50Aug 9, 2025Updated 6 months ago
Alternatives and similar repositories for seq2HLA
Users that are interested in seq2HLA are comparing it to the libraries listed below
Sorting:
- Fast and accurate in silico inference of HLA genotypes from RNA-seq☆154Aug 20, 2024Updated last year
- This Is Indian Country - Spring 2018 Instance☆12Apr 30, 2018Updated 7 years ago
- a R package to identify neoantigens from NGS data☆19Jun 29, 2017Updated 8 years ago
- Using k-mers to call HLA alleles in RNA sequencing data☆23Jul 26, 2018Updated 7 years ago
- ☆13Sep 30, 2024Updated last year
- Nextflow pipeline for Mutect2 somatic variant calling best practices☆23Jun 14, 2024Updated last year
- EasyFuse is a pipeline for accurate fusion gene detection from RNA-seq data.☆64Feb 13, 2026Updated 2 weeks ago
- cfSNV: An R tool of sensitively detecting tumor mutations from cell-free DNA in blood☆14Apr 29, 2023Updated 2 years ago
- Individual level Differential Expression Analysis for Single cells☆26Dec 24, 2022Updated 3 years ago
- A easy-to-use Python API for Primer3 primer design.☆16Nov 10, 2022Updated 3 years ago
- Combined mutation recurrence and functional impact to identify coding and non-coding cancer drivers☆15Oct 26, 2018Updated 7 years ago
- Fork from https://bitbucket.org/mcgranahanlab/lohhla/src, modified for MSKCC needs☆32Jul 27, 2023Updated 2 years ago
- HLA typing for Sanger Based Test☆19Apr 7, 2023Updated 2 years ago
- ☆26Apr 1, 2025Updated 11 months ago
- curPrimers is a tool for trimming primer sequences from amplicon based NGS reads☆17May 26, 2025Updated 9 months ago
- Github for files currently published in the IPD-IMGT/HLA FTP Directory hosted at the European Bioinformatics Institute☆251Feb 11, 2026Updated 2 weeks ago
- Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan.☆115Sep 2, 2024Updated last year
- DNA and RNA variant calling pipelines with HLA typing and Neoantigen predictions☆11Jul 8, 2021Updated 4 years ago
- Msuite2: integrated DNA methylation data analysis toolkit with enhanced performance☆10Jan 21, 2025Updated last year
- Precision HLA typing from next-generation sequencing data☆210Mar 5, 2024Updated last year
- ☆41Aug 18, 2020Updated 5 years ago
- ☆19Feb 20, 2018Updated 8 years ago
- A Java package for non-invasive cancer diagnosis using methylation profiles of cell-Free DNA.☆16Apr 2, 2019Updated 6 years ago
- Create mutation signatures from MAF's, and decompose them into Stratton signatures☆60Jun 7, 2019Updated 6 years ago
- Clonal and subclonal Copy Number Alteration quality check integrating somatic mutation☆25Jan 28, 2026Updated last month
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆100Apr 20, 2021Updated 4 years ago
- Immune Cell Gene Signatures for Profiling the Microenvironment of Solid Tumours☆28Jan 9, 2021Updated 5 years ago
- Bayesian-based fetal genotyping using maternal cell-free DNA and parental sequencing data.☆14Jun 5, 2019Updated 6 years ago
- Testing a neutral evolution model on cancer sequencing data☆10Feb 17, 2021Updated 5 years ago
- scMalignantFinder is a Python package specially designed for analyzing cancer single-cell RNA-seq datasets to distinguish malignant cells…☆17Feb 20, 2026Updated last week
- ☆14Oct 24, 2025Updated 4 months ago
- Python-based framework for computational immunomics☆40Jul 7, 2021Updated 4 years ago
- TCRconv is a deep learning model for predicting recognition between T cell receptors and epitopes. It uses protBERT embeddings for the TC…☆26Oct 18, 2022Updated 3 years ago
- SelectiOn in PRotein ANnotated regiOns. Adapted dN/dS based method to detect selection in specific protein regions☆11May 2, 2024Updated last year
- Tests Allelic Expression data for extreme imbalance w.r.t. population☆11Oct 8, 2021Updated 4 years ago
- Tool for analyzing the inter-mutational distances between SNV-SNV and INDEL-INDEL mutations. Tool separates mutations into clustered and …☆14Feb 16, 2026Updated 2 weeks ago
- A webtool for the clinical interpretation of CNVs in rare disease patients☆13Jun 10, 2022Updated 3 years ago
- NGSeminar on the use of Jupyter and R notebooks in biomedical research☆13Jan 28, 2023Updated 3 years ago
- MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.☆383Feb 18, 2026Updated last week