Pathways and networks Tools

Model based analysis for chip-seq data

Peak-caller for CLIP- and RIP-Seq high-throughput protein-RNA interaction data. It accepts input in BED or BAM format and identifies regions of significant enrichment for reads. It can also optionally incorporate additional external covariates into the peak-calling process, and identify sites of differential binding occupancy between cell types, conditions or development stages.

Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data