Tools

TOLM

Time-ordered linear model (TOLM) is feature-reduction method based on the idea that a co-bisector can represent the main tendency of a series of vectors. This co-bisector model has two main advantages: first, unlike present methods such as PCA, the co-bisector model conserves the temporal properties of a series of vectors since they have order-restricted projection locations on the co-bisector. Second, TLM preserves the spatial distance ratio between neighboring samples which have fixed locations in a abstract cell state space.

Citation:

Estimating developmental states of tumors and normal tissues using a linear time-ordered model. BMC Bioinformatics201112:53

 

M&M

M&M is a novel integrative statistical framework (for integration of MeDIP-seq and MRE-seq) that dynamically scales, normalizes, and combines MeDIP-seq and MRE-seq data to detect differentially methylated regions in a genome-wide fashion.M&M leverages the complementary nature of MeDIP-seq and MRE-seq data to allow rapid comparative analysis between whole methylomes at a fraction of the cost of WGBS.

Citation:
Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm. Genome research 23 (9), 1522-1540

 

FeatSNP (testing)

Functional epigenetic annotation tool of SNP (FeatSNP) is a online tool that collects functional and epigenetic annotation of human SNP.