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Yu S. Huang's Projects

accucopy icon accucopy

Accucopy is a computational method that infers Allele-Specific Copy Number alterations from low-coverage low-purity tumor sequencing data.

accurity icon accurity

Accurity is a computational method that infers tumor purity and tumor cell ploidy from tumor-normal WGS (whole exome will probably work too) data by jointly modelling SCNAs and heterozygous germline single-nucleotide-variants (HGSNVs).

annot icon annot

the old annot svn repository

egada icon egada

An enhanced version of GADA, a fast and sparse segmentation algorithm

eig icon eig

Eigen tools by Nick Patterson and Alkes Price lab

fastahack icon fastahack

utilities for indexing and sequence extraction from FASTA files

fsom icon fsom

A tiny C library for managing SOM (Self-Organizing Maps) neural networks

gatk icon gatk

This is Yu Huang's fork of GATK tag=1.6 Repository, https://github.com/broadgsa/gatk. Choose 1.6 because GATK source code started to be closed after that. Multiple custom java functions utilizing GATK libraries.

goio icon goio

IO related classes/functions

gwasmodules icon gwasmodules

Automatically exported from code.google.com/p/gwasmodules

pegaflow icon pegaflow

Pegasus Python3 APIs and the helper class Workflow.py

polyactis icon polyactis

EIG 3.0 C code and some Dockerfile. Automatically exported from code.google.com/p/polyactis

pymodule icon pymodule

A repo that contains miscellaneous Python/C++ modules/programs, a standalone Python module 'palos' by the yfish group (can be installed by pip).

pysam icon pysam

Automatically exported from code.google.com/p/pysam

repos icon repos

old namesake svn repository,

repository icon repository

repository contains a GOInformativeNode program, from old namesake svn repository

rust-book icon rust-book

Code for the Rust book https://doc.rust-lang.org/book/title-page.html

shell icon shell

a bunch of shell/python utilities program, was in a private svn repository before

sr2julia icon sr2julia

Port of Statistical Rethinking (2nd edition) code to Julia

sr2turingpluto.jl icon sr2turingpluto.jl

StatisticalRethinking notebook project using Turing and Pluto notebooks (derived from Max Lapan's Jupyter project)

test icon test

A playground to test different programming languages.

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