CNIT is designed for Affymetrix GeneChip to analyze copy number of each SNP allele. CNIT can be applicable in chromosome-abnormal disease, cancer and copy number variation studies, and can provide accurate CN estimations with low false-positive rate.
::DEVELOPER
Cathy S.J. Fann lab,Institute of Biomedical Informatics, National Yang-Ming University, Taipei
LocalNgsRelate is a software , which can be used to infer IBD sharing along the genomes of two individuals from low-depth Next Generation Sequencing (NGS) data by using genotype likelihoods (instead of called genotypes).
PoolHap2 is a computer program that infers haplotype (or epitype in case of DNA methylation sequencing) from a pool. In its current release, only pathogen sequencing application is implemented. In pathogen studies utilizing next generation sequencing, investigators ofte n collect samples naturally as pools of multiple strains, e.g., when the samples are taken from patients’ blood. To analyze these types of within-host polymorphisms, one would ideally like to determine the haplotypes in the sample. Even though isolation of single strains is possible by time-consuming experiments, the haplotype frequencies of different pathogen strains within a host are usually unknown, and this may well alter the initial within-sample frequencies. Here we developed Poolhap, a tool enabling researchers to infer the strain numbers and haplotype frequencies in silico from sequences of pooled samples.
The PoolHapX program reconstructs haplotypes within-host from pooled-sequencing data by integrating population genetic models (statistical linkage disequilibrium) with genomics reads (physical linkage). It approximate the resolution of single-cell sequencing using only pooled sequencing data, enabling within-host evolution analyses.
NARROMI is a MATLAB program for inferring gene regulatory networks from gene expression data. It is a novel method combining ordinary differential equation based recursive optimization (RO) and information-theory based mutual information (MI).
CMI2NI (CMI2-based network inference) is a software for inferring gene regulatory networks from gene expression data. It is a novel method using a new proposed concept of Conditional Mutual Inclusive Information (CMI2) which can accurately measure direct dependences between genes. Given the small size samples of gene expression data, CMI2NI can not only infer the correct topology of the regulation networks but also accurately quantify the dependence or regulation strength between genes.
DynaDup is a Dynamic Programing based Java application for building species trees from gene trees minimizing gene duplication and gene duplication and loss.
LOX (Level Of eXpression) is a program that employs Markov Chain Monte Carlo to estimate level of expression from census sequencing data sets with multiple treatments or samples.