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2020-sisg-mcmc-exercises-eca

Exercises for Module 15

additive_epistasis

Collection of R, Python, Perl and Tensorflow programs to simulate and detect the additive epistasis genetic model

admixture_analysis

apoe-genotyper

Tool to gentoype allelic variants of ApoE protein using rs429358 and rs7412 from a phased VCF

bafcalculator

B-allele frequency calculator from WES data

bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

bhr

Suite of heritability and genetic correlation estimation tools for exome-sequencing data

breakdancer

SV detection from paired end reads mapping

canopy

cardiometabolic_prs_plasma_proteome

Source code and software list for the study "Integrative analysis of the plasma proteome and polygenic risk of cardiometabolic diseases" on bioRxiv (doi: 10.1101/2019.12.14.876474)

ccxt

A JavaScript / Python / PHP cryptocurrency trading library with support for more than 85 bitcoin/altcoin exchanges

courses

Course materials for the Data Science Specialization: https://www.coursera.org/specialization/jhudatascience/1

coverage

Python script for heatmap coverage plot

covid19_mr

Script for generating PRS scores for the collaborative COVID-19 research.

dall-e

PyTorch package for the discrete VAE used for DALL·E.

dask-tutorial-scipy-2018

Materials for "Parallelizing Scientific Python with Dask"

data-science-ipython-notebooks

Continually updated data science Python notebooks: Deep learning (TensorFlow, Theano, Caffe), scikit-learn, Kaggle, Spark, Hadoop MapReduce, HDFS, matplotlib, pandas, NumPy, SciPy, Python essentials, AWS, and various command lines. https://bit.ly/data-notes

dddmaps

Mutability adjusted proportion of singletons calculation using synonymous SNPs from the DDD unaffected parents.

dddnoncoding2017

Code for paper published in March, 2017 analysing the role of de novo mutations in severe developmental disorders (part of the deciphering developmental disorders project).

deepmind-research

This repository contains implementations and illustrative code to accompany DeepMind publications

fasta-manipulation

fiveminutestats

A repo of short "vignettes" illustrating statistical concepts

flashpca

Fast Principal Component Analysis of Large-Scale Genome-Wide Data

gene-ages

Consensus ages for genes

genomicsem

R-package for structural equation modeling based on GWAS summary data

giab_remap_38

Remap the Genome in a Bottle NA12878 validation variant calls to human genome build 38

gwas-pw-paper

h2-gre

Implemention of Accurate estimation of SNP-heritability from biobank-scale data irrespective of genetic architecture.

hap.py

Haplotype VCF comparison tools

hess

Estimate local SNP heritability and genetic covariance from GWAS summary association statistics.