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Genetic Analysis: GWAS Genetic Variation Linkage Analysis Gene Expression
Sequence Analysis: Assembly Annotation Alignment RNAi RNA-seq Primer Design Next Generation Tools Phylogenetic Analysis Gene Structure Viral
HLA typing from exome capture sequencing.
GenePattern is a powerful genomic analysis platform that provides access to hundreds of tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research..
Heritability Calculator (HC) is a comprehensive package enabling the calculations of epidemiological and genetic parameters (such as broad/narrow sense heritabilities, true and population based heritability estimates, familial relative risk, marginal and epistatic effect size, detection power) for general (non-additive) genetic architectures.
MAGENTA is a program that tests whether predefined biological processes or gene sets are enriched for genes associated with a complex disease or trait.
Pilon uses read alignment analysis to diagnose, report, and automatically improve genome assemblies, and it can also be used to make variant calls among similar haploid strains.
SNAP is a web server for finding and annotating proxy SNPs based on linkage disequilibrium, genomic location, and coverage by commercial genotyping arrays.
Tagger is a web server for the selection and evaluation of tag SNPs from genotype data.
V-Phaser is a tool to call variants in mixed populations from ultra-deep sequence data. V-Phaser combines information regarding the covariation (i.e. phasing) between observed variants to increase sensitivity and an expectation maximization algorithm that iteratively recalibrates base quality scores to increase specificity. V-Phaser can reliably detect rare variants in mixed populations that occur at frequencies of <1%. The V-Phaser package also includes V-Profiler a tool to analyze and visualize variants.