Myrna is a cloud computing tool for calculating differential gene expression in large RNA-seq datasets. Myrna uses Bowtie for short read alignment and R/Bioconductor for interval calculations, normalization, and statistical testing. These tools are combined in an automatic, parallel pipeline that runs in the cloud (Elastic MapReduce in this case) on a local Hadoop cluster, or on a single computer, exploiting multiple computers and CPUs wherever possible.
miR_Path is a software for inferring cancer-related miRNAs based on gene expression data. It is a novel computational framework to identify the cancer-related miRNAs based solely on gene expression profiles which can effectively identify cancer-related miRNAs with higher precision compared with other popular approaches.
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.
CAFE (Chromosomal Aberration Finder in Expression data) is an R package for the detection of gross chromosomal gains and losses from expression microarrays, with a resolution up to cytoband level.
Babelomics is a complete suite of web tools for the functional profiling of genome scale experiments, with new and improved methods as well as more types of functional definitions. Babelomics includes different flavours of conventional functional enrichment methods as well as more advanced gene set analysis methods that makes it a unique tool among the similar resources available.
Pathprint integrates pathway curation, profiling methods, and public repositories, to represent any expression profile as a ternary score (-1, 0, +1) in a standardized pathway panel.