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exome-utilities

Utilities for Exome Sequencing, annotation, inferred relatedness errors, and gender mismatches

fast-lmm

Python version of Factored Spectrally Transformed Linear Mixed Models

fasta_file_manipulation

fatdistngwas

Code and data related to the meta-analysis of fat distribution in UK Biobank and GIANT

genbankr

gene_lists

List of gene lists for genomic analyses.

genemoduleannotation

genetest

Python package for efficient genetic association analyses

genipe

Genome-wide imputation pipeline

gephi

Gephi - The Open Graph Viz Platform

github_and_rmd_introduction

An introduction to using git and R markdown to document projects

glnexus

Scalable gVCF merging and joint variant calling for population sequencing projects

goodreads_textmining

Webscraping and analyzing book reviews on GoodReads

gsva

Gene set variation analysis for microarray and RNA-seq data

gvcf2vcf

Convert gVCF to VCF

gwa_tutorial

A comprehensive tutorial about GWAS and PRS

gwas_catalog

R-readable GWAS Catalog with scripts to digest it

gwas_qc

gwas_scripts

Codebook from my GWAS cookbook

hgvs

HGVS variant name parsing and generation

imputationserver

Michigan Imputation Server: A new web-based service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity

intervar

A bioinformatics software tool for clinical interpretation of genetic variants by the 2015 ACMG-AMP guideline

isaac_variant_caller

jami

Java tool for computing conditional mutual information from large datasets

jeffheaton-book-code

Source code from my older (pre Artificial Intelligence for Humans books) books. I am no longer updating these older editions.

jenior_metatranscriptomics_msphere_2018

Repository associated with Jenior ML, et al. (2018). mSphere.

lb-seq

Liquid Biopsy Sequencing analysis tools for cell free DNA sequencing

ldavis

ldpred

learning-spark-examples

Examples for learning spark