Search Results for "haplotype"
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Showing 22 open source projects for "haplotype"
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HubSpot is an AI-powered customer platform with all the software, integrations, and resources you need to connect your marketing, sales, and customer service. HubSpot's connected platform enables you to grow your business faster by focusing on what matters most: your customers.
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Evolia is a web and mobile platform that connects enterprises with 1000’s of local shift workers and offers free workforce scheduling and time and attendance solutions. Is your business on Evolia?
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5.Kernelized qtl-haplotype mapping (HPC)
Fortran/R program for kernelized qtl-haplotype mapping by mixed model
Kernelized qtl-haplotype mapping (named KHAMMIX) is a Fortran/R program which performs parallel haplotype based scans of chromosomes, by mixed model analyses, for diploid organisms. Two kernels; the Gaussian and Van Raden kernels, are allowed for the mixed model analyses. The haplotypes are defined by a sliding window of L SNP markers (L is an integer greater or equal to 1). Hence, 2^L haplotypes can be (not necessarily) observed for a sliding window (e.g. 2^6=64 for L=6). Reference: http... -
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HapAltMin
Haplotype assembly software using Alternating Minimization Algorithm
HapAltMin is a Haplope assembly software based on the principles of Binary Matrix Completion using Alternating Minimization Iterative Procedure. This software takes as input the Haplotype-relevant Fragment files and phases haplotypes for diploid organisms. -
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BamBam
Tools for genomic analysis
BamBam includes numerous tools for analyzing DNA next-generation sequencing data. Tools are provided for calling SNPs and indels, identifying large scale deletions, tabulating counts of mapped reads, methylation analysis, and more. Depends on SAMtools (http://samtools.sourceforge.net/) and BAMtools (https://github.com/pezmaster31/bamtools). Also uses BioPerl, which is included in the download tarball. -
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GSA-SNP is a gene set analysis software that can process SNP data as well as gene and haplotype data.
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Collaborate is customizable case management software for non-profits and social services agencies with teams of 5+ staff.
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GetSynth
A toolkit for haplotype synthesis analysis
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HaploView is a Java based tool for use by biologists in the study of genetic haplotype data. It provides a quick, easy interface to many common tasks involved in such analyses. Please go to the homepage below for the latest version!
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2bRAD-denovo
THIS REPOSITORY HAS BEEN MOVED TO GITHUB
Download the latest updates from https://github.com/z0on/2bRAD_denovo 2bRAD is a method for cost-efficient whole-genome genotyping, described in Wang et al 2012 http://www.nature.com/nmeth/journal/v9/n8/abs/nmeth.2023.html This project is about analyzing 2bRAD data without a genome reference. Scripts and walkthroughs for: - trimming and quality filtering; - removing PCR duplicates; - assembling loci; - calling variants (SNP-wise and haplotype-wise); - recalibrating quality... -
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BFBP
Bit flipping and belief propagation algorithms for haplotype assembly
Bit flipping and belief propagation algorithms for haplotype assembly -
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bioluminescence
A java library for polymorphic genome assembly.
Bioluminescence is a java library for facilitating de novo genome assembly in the context of reads sampled from a single highly-polymorphic diploid individual. Bioluminescence implements a novel algorithm which uses an artificial neural network to classify contigs in a genome assembly as haplotype-specific or not-haplotype-specific. It then uses this information to partition the original input read set into two subsets, each of which has been enriched for one of the haplotypes. Initial results... -
ConnectWise ScreenConnect, formerly ConnectWise Control, is a remote support solution for Managed Service Providers (MSP), Value Added Resellers (VAR), internal IT teams, and managed security providers. Fast, reliable, secure, and simple to use, ConnectWise ScreenConnect helps businesses solve their customers' issues faster from any location. The platform features remote support, remote access, remote meeting, customization, and integrations with leading business tools.
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virHap
A Software package for Inferring the haplotype structure of a mixed vi
PhyVar is an open-source software package for viral quasi-species reconstruction, which makes use of a novel phyloprobabilistic approach to infer the sub clonal composition and evolutionary history of a viral population from NGS data. The program aims to characterize and quantify the composition, the abundance and the evolutionary path of the underlying viral population within a given host by analyzing Next Generation Sequencing data. The program takes as input the collection of reads... -
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Phacro
Phasing haplotype and Crossover inferring
Phasing the haplotype of an individual with her oocyte or his sperm single cell sequencing data, and identify the crossover positions on oocytes or sperms. -
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GERMLINE
Algorithm for discovering long shared segments of IBDs in populations.
GERMLINE is an algorithm for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population. It takes as input genotype or haplotype marker data for individuals (as well as an optional known pedigree) and generates a list of all pairwise segmental sharing. -
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SOAPsv
SOAPsv: is a program for detecting the structural variation
This is an approach that complements previous methods for reliable homozygous structural variation identification. Our approach accurately determines genotype and breakpoints relative to a reference genome based on de novo assembly of Illumina Genome Analyzer sequencing data. In this method, we examined only homozygous structural variations because detecting heterozygous structural variations requires assembly of haplotype sequences, which is not yet possible using existing assemblers. -
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Diversity Maps is a data visualization tool for plant geneticists and breeders. It generates publication-quality, vector-based chromosome maps displaying differences in marker states between individuals.
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HATS (Haplotype Amplification in Tumor Sequences) is a tool that calls the amplified alleles, and thus amplified haplotype, in copy number aberration regions in next generation sequencing tumor data. The amplified haplotype may reveal gene variants.
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The annotation files for Illumina SNP genotyping platforms generated for performing Homozygosity Haplotype analysis
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HaploPainter - a pedigree and haplotypes drawing tool written in Perl/Tk. The software processes pedigree information in standard linkage formats combining haplotype information outputs from Simwalk, Genehunter, Allegro and Merlin.
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a cross-platform framework and environment for haplotype analysis with a special focus on human and medical genetics in python/wxpython
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The phase machine program allows supervised classification of DNA sequence data from different populations using haplotype sequences generated by the PHASE program.
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HapSnap computes common haplotypes in a human population from SNP allele frequency. Its main advantage over genetype-based haplotype estimation is speed, both in terms of molecular data generation and computation. Its main drawback is reduced accuracy.
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MAGMA: Multiobjective Analyzer for Genetic Marker Acquisition A genetic algorithm for generating SNP tiling paths from a large SNP database based on the competing objectives of cost (number of SNPs) and coverage (haplotype blocks): Hubley R., Zitzler
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