Python wrapper and web-server for Ensembl VEP

Predictive marker discovery for groups; binary data, genomic data (single nucleotide variants), arbitrary character data.

A simple module for diagnostic variant information parsing

Single Nucleotide Variant Filtering

Note: This is a detailed Intro to this project. A brief users guide can be found at users_guide.md

Multi-bAse Codon-Associated variant Re-annotatiON (MACARON)

Dockstore implementation of CGP core WXS analysis

Dockstore implementation of CGP core WGS analysis

xGAP is an efficient, modular, extensible and fault-tolerant pipeline for massively parallelized genomic analysis/variant discovery from next-generation DNA sequencing data.

TCGA hg19 and hg38 data downloader.

Front-End for SNV Business firm

Cell Line Authentication from ChIP-seq data

Extract and explore snv data

cfDNApipe: A comprehensive quality control and analysis pipeline for cell-free DNA high-throughput sequencing data

Pipeline to call SNV's with 4 tools (VarDict, LoFreq, Mutect2 & SiNVICT)

Estimates the clonal population structure in a tumour sample given a cell mutation matrix

acorn is an R package that examines various features of de novo variants including subsetting DNVs by individual, variant type, or genomic region; calculating features including variant change counts, lengths, and presence/absence at CpG sites; and characteristics of parental age and number of DNVs.

GATK WGS workflow

Pipeline for gene candidate discovery based on mutagenesis. Featured in gene cloning research published in Nature (DOIs: 10.1038/s41467-020-14937-2, 10.1038/s41467-021-23738-0, 10.1038/s41477-021-00971-5), Molecular Plant (DOI: 10.1016/j.molp.2021.05.010) and New Phytologist (DOI: 10.1111/nph.17075).