felixfan / PyHLA
Python for HLA analysis: summary, association analysis, zygosity test and interaction test
☆34Updated 9 months ago
Alternatives and similar repositories for PyHLA:
Users that are interested in PyHLA are comparing it to the libraries listed below
- Burden testing against public controls☆50Updated last year
- This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…☆52Updated 4 years ago
- Create mutation signatures from MAF's, and decompose them into Stratton signatures☆60Updated 5 years ago
- identifying mutational significance in cancer genomes☆61Updated 2 years ago
- CNV screening and annotation tool☆25Updated 8 years ago
- CADD scripts release for offline scoring. For more information about CADD, please visit our website☆80Updated 4 months ago
- Workflows for converting between sequence data formats☆38Updated 3 years ago
- ☆25Updated 5 years ago
- Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer☆97Updated 4 years ago
- ☆41Updated last year
- Fork of the Polysolver project☆31Updated 5 years ago
- ☆53Updated 2 years ago
- CN-Learn☆29Updated 5 years ago
- Scripts to run copynumber variation calls on tumor and normal BAM files using Varscan2☆29Updated 7 years ago
- DEPRECATED. This tool has been superseded by https://github.com/griffithlab/pVACtools☆61Updated 6 years ago
- ClassifyCNV: a tool for clinical annotation of copy-number variants☆62Updated last year
- DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated ma…☆49Updated 2 years ago
- Somatic copy number analysis using WGS paired end wholegenome sequencing☆70Updated 4 years ago
- ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to ama…☆21Updated 2 years ago
- This method uses shallow Whole Genome Sequencing (sWGS) and the segmentation of a genomic profile to assess the Homologous Recombination …☆34Updated 9 months ago
- utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.☆48Updated 5 years ago
- Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.☆97Updated 2 years ago
- Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests☆49Updated 8 months ago
- Scripts involved in our workflow for detecting CNVs from WGS data using read depth-based methods☆46Updated 2 years ago
- This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are al…☆78Updated 5 years ago
- SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, …☆45Updated 3 weeks ago
- Create "haplotype maps" of variants in order to use with Picardtools Crosscheck_Files utility, which allows for robust genotyping of func…☆28Updated last year
- Exome/Capture/RNASeq Pipeline Implementation using snakemake☆45Updated 7 years ago
- Documenting usage and experience with bioinformatic tools☆41Updated 9 years ago
- A simplified pipeline for ctDNA sequencing data analysis☆36Updated 7 years ago