Cancer variant data from genome-wide association studies (GWAS)

A collection of scripts and notes related to genomics and bioinformatics

Cancer Predisposition Sequencing Reporter (CPSR)

Personal Cancer Genome Reporter (PCGR)

Tillandsia phylogenomics and hybridization, Yardeni et al., 2025

An easy-to-use Python tool for visualizing multi-sample VCF SNP genotypes as a categorical heatmap, where homozygous reference, heterozygous, homozygous alternate & missing data are color-coded. Ideal for genetic studies, comparative analyses & QC of variant data.

R package for working with vcf files

A streamlined pipeline for germline variant calling on chromosome 11 using GATK. This repository includes workflows for data preprocessing, variant discovery, and annotation, with a focus on understanding genetic variations linked to disease-associated genes.

An R package and Web App for efficient quality control of human whole-genome and whole-exome datasets

A simple tool for SNP mutation type determination.

Population Genomics Pipeline used for SNPs data from VCF files.

Repository for RecallME-v.0.1 a variant calling pipelines benchmarker and optimizer

Read/write VCF contact files with R

Splicing Prediction Pipeline

Scripts in R for analyses of Isolation by Distance (IBD) - PART 2 in LANDSCAPE GENOMICS PIPELINE

Scripts in R for Landscape Genomics Analyses v.2

visual analysis of your VCF files

A variant annotation tool that parses vcf files and fetches variant information from the Ensembl Variant Effect Predictor (VEP) REST API

R-based pipeline/script to implement a Genome-Wide Association Study (GWAS) analysis based on the RAINBOWR package

The goal of this project is to create a R package and executable scripts to visualize variants in Variant Call Format (VCF) files and Bcftools processed tab-delimited files.