TRON-Bioinformatics / seq2HLA
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.
☆48Updated last year
Alternatives and similar repositories for seq2HLA:
Users that are interested in seq2HLA are comparing it to the libraries listed below
- Public repository containing research code for the TCGA PanCanAtlas Splicing project☆41Updated 4 years ago
- ☆116Updated last year
- Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent gen…☆27Updated 4 years ago
- Genomic Identification of Significant Targets in Cancer (GISTIC), version 2☆49Updated 2 years ago
- Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)☆75Updated last year
- Fork of the Polysolver project☆30Updated 5 years ago
- A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior …☆62Updated last week
- An R package to time somatic mutations☆60Updated 4 years ago
- ☆71Updated 9 months ago
- nextNEOpi: a comprehensive pipeline for computational neoantigen prediction☆68Updated 2 months ago
- HMMRATAC peak caller for ATAC-seq data☆100Updated 3 months ago
- ☆37Updated 4 years ago
- Estimate locus specific human LINE-1 expression.☆32Updated 2 years ago
- ☆77Updated last year
- mutation(barcode) caller for 10x single cell data☆44Updated 4 years ago
- Code and additional processed data for manuscript "Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab"; see for man…☆51Updated 7 years ago
- identifying mutational significance in cancer genomes☆60Updated 2 years ago
- ☆57Updated 4 years ago
- ☆47Updated last month
- CADD scripts release for offline scoring. For more information about CADD, please visit our website☆76Updated 2 months ago
- DEPRECATED. This tool has been superseded by https://github.com/griffithlab/pVACtools☆61Updated 5 years ago
- Dynamics analysis of Alternative PolyAdenylation from RNA-seq☆55Updated last year
- Convert Counts to Fragments per Kilobase of Transcript per Million (FPKM)☆62Updated 3 years ago
- ☆110Updated last year
- Somatic copy number analysis using WGS paired end wholegenome sequencing☆70Updated 4 years ago
- Tutorial Website☆56Updated 4 years ago
- A modular, containerized pipeline for ATAC-seq data processing☆55Updated last week
- nucleosome calling using ATAC-seq☆106Updated 4 years ago
- An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.☆70Updated 8 months ago
- Create mutation signatures from MAF's, and decompose them into Stratton signatures☆60Updated 5 years ago