Statistical Genomics

EIGENSOFT: This software package uses principal components analysis to infer genetic ancestry and correct for population stratification in case-control studies

HAPMIX: This is a method for accurately inferring chromosomal segments of distinct continental ancestry in admixed populations, using dense genetic data

PBAT: An interactive software package that provides tools for the design and the data analysis of family-based association studies

PowerGxE: Power Calculations for Genetic Association Tests Exploiting Gene-environment Interaction

Microarray Data Analysis

AMP: Automated Microarray Pipeline, a tool for normalizing microarray data.

dChip: Analysis and visualization of gene expression and SNP microarrays

FuncAssociate: This program takes a list of genes as input and produces a ranked list of the Gene Ontology terms enriched in an input list.

GCOD: GeneChip Oncology Database, a collection of curated cancer-related microarray studies, collected from published datasets.

MAT: A model-based algorithm for finding enriched regions in ChIP-Chip experiments

TM4: Microarray analysis suite including Microarray Data Manager, Automated Microarray Pipeline, MultiExperiment Viewer, Microarray Data Analysis System, and Spotfinder.

Biosequence Data Analysis

BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes

MDscan: A fast and accurate motif finding algorithm with applications to chromatin immunoprecipitation microarray experiments

MotifRegressor: A program for finding DNA sequence motifs

Biological Annotations and Databases

FooFunc: A web-based software for browsing quantitative gene function assignments for yeast and mouse genes.

Gene Index Project: An inventory of likely genes and their variants and to annotate these with information regarding the functional roles played by these genes and their products

GeneSigBD: a searchable database of fully traceable, standardized, annotated gene signatures which have been manually curated from publications that are indexed in PubMed

RESOURCERER: A microarray-resource annotation and cross-reference database built using the analysis of expressed sequence tags (ESTs) and gene sequences.

Synergizer: A database of gene, protein, and other biological identifiers coupled to a web interface that allows users to translate names from one identifier system to another.

Statistical Analysis

SPMM: SAS Macros to fit smoothing splines mixed models

More software packages from Program Faculty

“Computational_Biology”Jun Liu

Shirley Liu

Peter Kraft

John Quackenbush

Frederick Roth