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23andme-to-vcf

A command line utility to convert 23andme raw data files to VCF format

4dvous

Genomic regions annotation using 4D Genome data

aberrant

Aberrant R package from https://www.well.ox.ac.uk/~spencer/Aberrant/

bamdst

a lightweight bam file depth statistical tool

computational.biology

quick Manhattan plot app

gassocplot2

Second version of gassocplot: a regional association plotter for genetic and epigenetic data

grep

GREP: Genome for REPositioning drugs

gwasdb

fast query of gwas result stored in sql

icarus

Species identification and resistance genes mapping from ONT long reads

impute-me

This is the code behind the www.impute.me site. It contains algorithms for personal genome analysis, including imputation and polygenic risk score calculation

m3c

Monte Carlo Reference-based Consensus Clustering

mungesumstats

Rapid standardisation and quality control of summary statistics from GWAS

n2v-hc

nandobonf.github.io

nf-bam2fastq

Nextflow-based BAM-to-FASTQ conversion and FASTQ-sorting workflow.

ngspipe

pipeline for analysis of NGS data

pathifier-tool-kit

Scripts that may help you use PATHIFIER (Drier et al., 2013)

pcamatchr

A flexible R package for weighted principal component case control matching

racer

An R package for generating comparative regional association plots

se-mei

Tools for finding mobile element insertions from single-end datasets

signaturesearch

R/Bioconductor package including the Gene Expression Signature Search (GESS), Function Enrichment Analysis (FEA) methods and supporting drug-target network construction for visualization

snpsettest

A set-based association test using GWAS summary statistics

somalier

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

star_protocols_core_modules

Code accompanying STAR protocols publication describing the identification of core modules in a co-expression network using GWAS data

unicorn-qc

variants_in_homopolymer_regions

wecall

Fast, accurate and simple to use command line tool for variant detection in NGS data.