Search Results for "association"

TASSEL is a bioinformatics software package that can analyze diversity for sequences, SNPs, or SSRs. Genotype/phenotype associations can be carried out by GLM or a mixed model. Estimates distance and linkage disequilibrium statistics.

ParseCNV CNV call association software takes CNV calls as input and creates SNP based statistics for CNV occurrence in population study cases and controls then calls CNVRs based on neighboring SNPs of similar significance.

...A presence/absence matrix is also generated to allow you to identify the core/accessory genome content across all your genomes. The outputs generated by SPANDx can be imported into PLINK for microbial genome-wide association study (mGWAS) analyses. SPANDx can utilise PBS, SGE or SLURM for resource management. SPANDx can also run directly on the command line if no resource manager is available. For the most up-to-date version of SPANDx, check us out on GitHub: https://github.com/dsarov/SPANDx

PriorityPruner is a software program which can prune a list of SNPs that are in high linkage disequilibrium (LD) with other SNPs in the list, while preferentially keeping SNPs of higher priority (e.g., the most significant SNPs in a genome-wide association study).

...Here we present a novel software package GENIE, which utilizes the power of multiple GPU or CPU processor cores to parallelize the interaction analysis. Citation: Chikkagoudar, S., Wang, K., & Li, M. (2011). GENIE: a software package for gene-gene interaction analysis in genetic association studies using multiple GPU or CPU cores. BMC research notes, 4(1), 158.

MCPerm: A Monte Carlo permutation method for multiple test correlation in case-control association study Traditional permutation (TradPerm) test is an important non-parametric analysis method which can be treated as the gold standard for multiple testing corrections in case-control association study. However, it relies on the original single nucleotide polymorphism (SNP) genotypes and phenotypes data to perform a large number of random shuffles, and thus it is computationally intensive, especially for genome-wide association study (GWAS). ...

UNPHASED is a versatile application for performing genetic association analysis.

...Double Layered Learning for Biological Event Extraction from Text. In Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, Portland, Oregon, June. Association for Computational Linguistic

The SNP ratio test can assess significance of enrichment of significant associations in genome-wide association studies. Tests can be applied to pathways such as KEGG/GO, or user-defined pathways to test specific hypotheses. See link below for more.

BCAR is a library for the associative classification, which denotes "Boosting Class Association Rules". BCAR provides a general tool for classification tasks with various types of input data.

Collection of tools for performing robust case-control disease and quantitative trait association studies using Copy Number Variants- Latest version should now be downloaded from Bioconductor

Our software can test for HLA allele and amino-acid differences between two populations. It examines zygosity, tests for strongest association, interaction & linkage disequilibrium among amino acid epitopes.

The ExactFDR software package is an improvement of permutation-based False Discovery Rate (FDR) estimation methods that takes advantage from exact p-value computations for analyzing Genome-wide association studies data

WGAViewer is a suite of JAVA software tools that provides a user-friendly interface to annotate, visualize, and help interpret the full set of P values emerging from a whole genome association (WGA) study.

A program to model HapMap haplotypes in genetic association studies using tag SNP genotypes. Please visit http://www.ucd.ie/genepi/hapmixmap for more details.