Tools for Genomic Analysis

Corbin Jones

VCAKE Genome assembly using short reads

Fred Wright and Ivan Rusyn

FastMap Fast eQTL mapping in homozygous populations
SAFEGUI Tests for significance in gene expression data

Leonard McMillan and Wei Wang

NPute Genotype imputation
TreeQA Quantitative genome wide association mapping
HiDim viewer High Dimensional data visualization
snpBrowser QTL analysis, genetic diversity

Wei Sun

asSeq Allele-specific next -gen sequencing data (RNA-seq and ChIP-seq)
BPrimm Bayesian and Penalized regression in multiple loci mapping
genoCN Analyze copy number states and genotypes using high density SNP arrays
mixer A mixture model approach to analyze ChIP-chip or ChIP-seq data
permuteP Permutation p-value calculations for QTL mapping
eMap (v1.2 Feb 2nd, 2010) ( vignettes ) eQTL computation, visualization, integration
censorSIR Tools for applying Slice Inverse Regression in censored data.
eqtl.TF eQTL and transcription regulation.
GOFinder Find enriched G O terms or genes within a GO term or its offspring . Use GO data stored in MySQL data base.
ss.hmm Segmental semi-Markov model