GENETIC ANALYSIS LINKS
Visualization tools for analysis of Genomic data
Integrative Genomics Viewer
The Integrative Genomics Viewer (IGV) is a visualization tool to simultaneously
integrate and analyze multiple types of genomic data.
Go to Integrative Genomics Viewer
GALAXY
http://main.g2.bx.psu.edu/
Genetic analysis
Birdsuite
The Birdsuite is a fully open-source set of tools to detect and report SNP genotypes,
common Copy-Number Polymorphisms (CNPs), and novel, rare, or de novo CNVs in
samples processed with the Affymetrix platform.
Go to Birdsuite
Genome Analysis Toolkit
The Genome Analysis Toolkit (GATK) is a structured programming framework designed
to enable the rapid development of efficient and robust analysis tools for next-generation
DNA sequencers. The GATK solves the data management challenge by separating data
access patterns from analysis algorithms, using the functional programming philosophy
of Map/Reduce. Since the GATK’s traversal engine encapsulates the complexity of
efficiently accessing the next-generation sequencing data, researchers and developers are
free to focus on their specific analysis algorithms. This not only vastly improves the
productivity of developers, who can quickly write new analyses, but also results in tools
that are efficient and robust, and can benefit from improvements to a common data
management engine.
Go to GATK
Ultrasome
Ultrasome is an extremely efficient methodology for detecting gains and losses of
chromosomal material in DNA copy-number data. The program processes latest-
generation copy number arrays about 10,000 times faster than standard methods (e.g.,
CBS) while retaining comparable analyticaccuracy.
Go to Ultrasome
Genetic variation
EIGENSTRAT
EIGENSTRAT detects and corrects for population stratification in genome-wide
association studies using principal components analysis.
Contact EIGENSTRAT Support
Go to EIGENSTRAT
GRAIL
GRAIL is an algorithm to assess biological relationships between disease-associated
genetic variants.
Go to GRAIL
Haploview
Haploview is designed to facilitate the process of haplotype analysis by providing a
common interface to several tasks relating to such analyses.
Go to Haploview
Locusview
LocusView is a program for generating images of chromosomal regions annotated with
genomic features, experimental data, and analysis results.
Go to Locusview
PLINK
PLINK is a comprehensive toolset for statistical analysis in whole-genome association
studies.
Go to PLINK
Sweep
Sweep allows large-scale analysis of haplotype structure in genomes for the primary
purpose of detecting evidence of natural selection.
Go to Sweep
SNAP
SNAP is a web server for finding and annotating proxy SNPs based on linkage
disequilibrium, genomic location, and coverage by commercial genotyping arrays.
Go to SNAP
Tagger
Tagger is a web server for the selection and evaluation of tag SNPs from genotype data.
Go to Tagger
Linkage analysis
GeneHunter
GeneHunter is a tool for rapid extraction of complete multipoint linkage analysis using
both parametric and nonparametric approaches.
Go to GeneHunter
MapMaker3
MapMaker is a package containing a program for genetic linkage analysis and a program
for mapping genes underlying complex traits.
Go to MapMaker3
High-throughput image analysis
CellProfiler
CellProfiler cell image analysis software quantitatively measures phenotypes from
thousands of images automatically, usually for high-throughput image-based cell
screening experiments.
Go to CellProfiler
CellProfiler Analyst
CellProfiler Analyst data exploration and analysis software is designed for complex and
interactive exploration of multidimensional data, specifically from high-throughput
image-based experiments.
Go to CellProfiler Analyst
Expression analysis
GenePattern
GenePattern is a software package for the analysis of molecular profiles, e.g., genomewide microarray expression signatures. It includes a collection of analytic and
visualization tools, interfaces for the easy construction of analytic pipelines and
integration of new modules without additional programming. GenePattern is available for
MacOS, Windows, and Linux platforms.
Go to GenePattern
Gene Set Enrichment Analysis
GSEA is a computational method that determines if a given set of genes shows
statistically significant differences between two biological states. It is useful for
interpreting the results of gene expression studies.
Go to Gene Set Enrichment Analysis
GeneCruiser
GeneCruiser is an annotation tool that allows users to map genes from genomic databases
to Affymetrix probes, find information about Affymetrix probes in genomic databases,
and find where Affymetrix probes are located in the human genome.
Go to GeneCruiser
Connectivity Map
The Connectivity Map is a collection of genome-wide transcriptional expression data
from cultured human cells treated with bioactive small molecules and simple patternmatching algorithms that together enable the discovery of decisive functional connections
between drugs, genes, and diseases. This web interface is designed to allow biologists,
pharmacologists, chemists, and clinical scientists to use our analysis tools and access the
raw data.
Go to Connectivity Map
Other
Primer3