polyactis

Senior Director of Bioinformatics, Genecast Biotech. Modelling and alrogithms.

Shanghai

Pinned Repositories

Accucopy
Accucopy is a computational method that infers Allele-Specific Copy Number alterations from low-coverage low-purity tumor sequencing data.
Language:C++15 2 234
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).
Language:C++4 1 02
eGADA
An enhanced version of GADA, a fast and sparse segmentation algorithm
Language:C++0 1 00
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 2 01
goio
IO related classes/functions
Language:Go0 1 00
math508FilteringTheory
2007 class math508, Filtering Theory, HMM, Kalman Filters
Language:Python1 1 00
repos
old namesake svn repository,
Language:Python1 1 01
rust-book
Code for the Rust book https://doc.rust-lang.org/book/title-page.html
Language:Rust0 1 00
SR2TuringPluto.jl
StatisticalRethinking notebook project using Turing and Pluto notebooks (derived from Max Lapan's Jupyter project)
Language:HTML0 0 00
transfac
the old transfac utility repository
Language:GLSL1 2 01

polyactis's Repositories

polyactis/Accucopy
Accucopy is a computational method that infers Allele-Specific Copy Number alterations from low-coverage low-purity tumor sequencing data.
Language:C++15 2 234
polyactis/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).
Language:C++4 1 02
polyactis/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 2 01
polyactis/math508FilteringTheory
2007 class math508, Filtering Theory, HMM, Kalman Filters
Language:Python1 1 00
polyactis/transfac
the old transfac utility repository
Language:GLSL1 2 01
polyactis/autismgenetics
Automatically exported from code.google.com/p/autismgenetics
Language:Python0 0 10
polyactis/devzero-misc
Miscelaneous Goodies to share
Language:Shell0 0 00
polyactis/eGADA
An enhanced version of GADA, a fast and sparse segmentation algorithm
Language:C++0 1 00
polyactis/goio
IO related classes/functions
Language:Go0 1 00
polyactis/rust-book
Code for the Rust book https://doc.rust-lang.org/book/title-page.html
Language:Rust0 1 00
polyactis/SR2TuringPluto.jl
StatisticalRethinking notebook project using Turing and Pluto notebooks (derived from Max Lapan's Jupyter project)
Language:HTML0 0 00
polyactis/EIG
Eigen tools by Nick Patterson and Alkes Price lab
Language:C2 0
polyactis/fastahack
utilities for indexing and sequence extraction from FASTA files
Language:C++1 0
polyactis/gwasmodules
Automatically exported from code.google.com/p/gwasmodules
Language:Python0 01
polyactis/gwaswebinterface
Automatically exported from code.google.com/p/gwaswebinterface
Language:JavaScript0 0
polyactis/julia-prob-programming
Julia Probability Programming
Language:Jupyter Notebook1 0
polyactis/pegaflow
Pegasus Python3 APIs and the helper class Workflow.py
Language:Python1 0
polyactis/polyactis
EIG 3.0 C code and some Dockerfile. Automatically exported from code.google.com/p/polyactis
Language:C0 0
polyactis/polyactis.github.io
My website based on Jekyll https://www.yfish.org/
Language:HTML0 0
polyactis/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:Python1 0
polyactis/pysam
Automatically exported from code.google.com/p/pysam
1 155
polyactis/shell
a bunch of shell/python utilities program, was in a private svn repository before
Language:Shell1 0
polyactis/smithwaterman
smith-waterman-gotoh alignment algorithm
Language:C++1 0
polyactis/SR2Julia
Port of Statistical Rethinking (2nd edition) code to Julia
Language:Jupyter Notebook0 0
polyactis/test
A playground to test different programming languages.
Language:C1 0
polyactis/utility
the old svn utility repository
Language:Python1 0
polyactis/vcf
Variant Call Format parser library for Go
Language:Go1 0
polyactis/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++1 0
polyactis/vervet-web
Automatically exported from code.google.com/p/vervet-web
Language:Python0 0
polyactis/vimenv
derivative of Emrah Kostem's https://bitbucket.org/ekostem/vimenv/
Language:Shell1 0