polyactis

Discovered public repositories for polyactis in the GitHub catalog.

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polyactis/math508FilteringTheory

2007 class math508, Filtering Theory, HMM, Kalman Filters

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polyactis/fastahack

utilities for indexing and sequence extraction from FASTA files

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polyactis/smithwaterman

smith-waterman-gotoh alignment algorithm

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polyactis/fsom

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

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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

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polyactis/wdist

a fork of WDIST. WDIST (Weighted DISTance calculator) tool supporting the BGI Cognitive Genomics Lab's data analysis pipeline, and designed to grow into a full-scale replacement for PLINK (eta early 2014). Since it uses streaming algorithms instead of keeping the entire dataset in memory, it can handle much larger files without the need for e.g. tedious chromosome splitting. It also incorporates numerous micro- (and a few macro-) optimizations which collectively speed up most of PLINK's slowest functions by factors exceeding 100x (and sometimes even exceeding 1000x).

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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.

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