felixfan / PyHLA
Python for HLA analysis: summary, association analysis, zygosity test and interaction test
☆32Updated 3 months ago
Related projects ⓘ
Alternatives and complementary repositories for PyHLA
- This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…☆50Updated 4 years ago
- Create mutation signatures from MAF's, and decompose them into Stratton signatures☆60Updated 5 years ago
- Burden testing against public controls☆50Updated 8 months ago
- CNV screening and annotation tool☆24Updated 8 years ago
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆94Updated 3 years ago
- ☆50Updated last year
- Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2☆28Updated 6 years ago
- Documenting usage and experience with bioinformatic tools☆40Updated 9 years ago
- Fork of the Polysolver project☆30Updated 5 years ago
- Exome/Capture/RNASeq Pipeline Implementation using snakemake☆45Updated 6 years ago
- identifying mutational significance in cancer genomes☆60Updated 2 years ago
- Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.☆96Updated 2 years ago
- ☆38Updated 9 months ago
- Workflows for converting between sequence data formats☆37Updated 3 years ago
- Somatic copy number analysis using WGS paired end wholegenome sequencing☆69Updated 4 years ago
- ☆67Updated 2 years ago
- For biological deep sequencing data. Decompose a UCSC knownGenes/Ensembl GTF file into transcript regions (i.e. exons, introns, UTRs and…☆33Updated last year
- ☆65Updated last year
- DEPRECATED. This tool has been superseded by https://github.com/griffithlab/pVACtools☆61Updated 5 years ago
- This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are al…☆76Updated 4 years ago
- A preprocessing pipeline for ChIP-seq, including alignment, quality control, and visualization.☆27Updated 7 years ago
- Snakemake-based workflow for detecting structural variants in genomic data☆77Updated 9 months ago
- RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.☆36Updated 2 years ago
- ☆78Updated 10 years ago
- Public repository containing research code for the TCGA PanCanAtlas Splicing project☆41Updated 3 years ago
- DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…☆49Updated 2 years ago
- Microsatellite instability (MSI) detection for tumor only data.☆94Updated 6 months ago
- ☆37Updated last year
- An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.☆69Updated 5 months ago
- CN-Learn☆29Updated 4 years ago