polyactis

Yu S. Huang's repositories

Accucopy

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

Language:C++GPL-3.015 2 23

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).

Language:C++NOASSERTION4 10

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.

Language:Java1 20

math508FilteringTheory

2007 class math508, Filtering Theory, HMM, Kalman Filters

Language:PythonMIT1 10

transfac

the old transfac utility repository

Language:GLSL1 20

autismgenetics

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

Language:Python001

devzero-misc

Miscelaneous Goodies to share

Language:Shell000

eGADA

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

Language:C++GPL-3.0010

EIG

Eigen tools by Nick Patterson and Alkes Price lab

Language:C020

fastahack

utilities for indexing and sequence extraction from FASTA files

Language:C++010

goio

IO related classes/functions

Language:Go010

gwasmodules

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

Language:Python000

gwaswebinterface

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

Language:JavaScript000

julia-prob-programming

Julia Probability Programming

Language:Jupyter Notebook010

pegaflow

Pegasus Python3 APIs and the helper class Workflow.py

Language:PythonApache-2.0010

polyactis

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

Language:C000

polyactis.github.io

My website based on Jekyll https://www.yfish.org/

Language:HTMLMIT000

pymodule

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

Language:Python010

pysam

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

01 155

rust-book

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

Language:Rust010

shell

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

Language:Shell010

smithwaterman

smith-waterman-gotoh alignment algorithm

Language:C++010

SR2Julia

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

Language:Jupyter NotebookMIT000

SR2TuringPluto.jl

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

Language:HTMLMIT000

test

A playground to test different programming languages.

Language:C010

utility

the old svn utility repository

Language:Python010

vcf

Variant Call Format parser library for Go

Language:GoBSD-3-Clause010

vcflib

fork of Erik Garrison's vcflib. c++ library for parsing and manipulating VCF files, many command-line utilities. My modification is adding high-level APIs to make it easy to call. it's now dependent on some header files from https://code.google.com/p/gwasmodules/source/browse/#hg%2Fpymodule%2Finclude

Language:C++MIT010

vervet-web

Automatically exported from code.google.com/p/vervet-web

Language:Python000

vimenv

derivative of Emrah Kostem's https://bitbucket.org/ekostem/vimenv/

Language:Shell010