Free Download of Our Software Packages
Genomic,
Expression and Pathway Analysis
Statistical
Analysis of Human Nondisjunction Data
Sequence
Analysis
- RNASeqBias
An R package for detecting and correcting biases in RNA-Sequencing data. The download link contains the package, the manual and a "vignette" for quick start.
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Genomic,
Expression and Pathway Analysis
A LOw-Rank representation and Sparse regression for eQTL
mapping. This algorithm accounts for confounding factors such as unobserved
covariates, experimental artifacts, and unknown environmental perturbations.
- TFBphylo
An R package implementing a phylogenetic tree based method
to model the on/off rates of transcription factor binding (TFB) events, and
uses the EM algorithm to estimate model parameters.
- iFad
An R package
implementing a bayesian sparse factor model for the joint analysis of paired
datasets, the gene expression and drug sensitivity profiles, measured across
the same panel of samples, e.g. cell lines.
- FacPad
An R package implementing a Bayesian sparse factor model for
the inference of pathways responsive to drug treatment.
- M3
An improved SNP calling algorithm for
Illumina BeadArry Data.
- GWAS with MRF pathway
This is a program to …
Related Paper, Download - Cosine
An R package to extract the globally most discriminative sub-network from multiple gene expression datasets with integration of protein-protein interactions data
Related Paper, Download - VitaPad
A program to visualize and analyze pathways
Link to the software
Genetic
Linkage Analysis
- LD Mapping with Haplotype Data
A program of mapping disease genes (including location and confidence interval) by using haplotypes with disease mutation and the haplotypes without disease mutation (or allele frequencies in normal population).
Related Paper, Download - LD Mapping with Genotype Data
This is a program to mapping the disease gene (including location and confidence interval) by using multisite genotype data of case-control studies.
Related Paper, Download - Multiple TDT
a program to do the associate test (TDT type test for nuclear-family data) using several tightly linked markers simultanously
Related Paper, Download - QSAT
A Program for Quantitative Association Analysis
ReadMe (PDF), Related Paper, Download - Haplore
A Program for Haplotype Reconstruction in Pedigrees
ReadMe (PDF), Related Paper, Download - Haplore (Solaris version)
ReadMe (PDF), Related Paper, Download - Haplore (Linux version)
ReadMe (PDF), Related Paper, Download
Gene Array
Data Analysis
- BCLUST
A program to assess reliability of gene clusters from expression data by using consensus tree and bootstrap resampling method
ReadMe (PDF), Related Paper, Download - QAmerge
1.0e
Pooling replicated microarray datasets exported from QuantArray image analysis software.
ReadMe (PDF) , Download - GPmerge
4.0b
Pooling replicated microarray datasets exported from GenePix Pro image analysis software.
ReadMe (PDF) , Download - QAnalyzer
1.0
Statistical analysis of QuantArray data, including dye effect adjustment and ANOVA analysis.
ReadMe (PDF) , Download - QAnalyzer
1.0 LINUX NEW!!!
Statistical analysis of QuantArray data, including dye effect adjustment and ANOVA analysis.
ReadMe (PDF) , Download - GProcesser
3.0 NEW!!!!
Statistical analysis of GenePix data, including dye effect adjustment and ANOVA analysis.
ReadMe (PDF) , Download - GProcesser 2.0 LINUX NEW!!!!
Statistical analysis of GenePix data, including dye effect adjustment and ANOVA analysis.
ReadMe (PDF) , Download
Statistical
Analysis of human nondisjunction Data
- EM based
method
An EM based algorithm to estimate genetic distances and chiasma distribution for human UPD and trisomy data.
Related Paper, Download - HMM based method
A Hidden Markov model based algorithm to estimate genetic distances and chiasma distribution for human UPD and trisomy data.
Related Paper, Download
Population
Genetics
- Marker
Search Power Calculation
An R package to calculate statistical power of strategies detecting associated markers
Readme, Download (Zip file) Download (Tar.gz file) - Overall LD
A program to assess the overall Linkage Disequilibrium (LD) over several markers and assess the LD between groups of markers.
Related Paper, Download
Modifier
Gene Analysis
- siliColony
A program to estimate the probability that a modifier gene is responsible for the segregation of phenotypes.
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