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Examines epigenomic and transcriptomic next generation sequencing (NGS) data. Octopus-toolkit can be used for antibody- or enzyme-mediated experiments and studies for the quantification of gene expression. It can accelerate the data mining of public epigenomic and transcriptomic NGS data for basic biomedical research. This tool provides a private and a public mode: one to process the user’s own data, and the other to analyze public NGS data by retrieving raw files from the GEO database.

CISD / Chromatin Interaction Site Detector

Allows genome-wide identification of potential chromatin– chromatin interaction (CCI) sites and loops at kilobase resolution. CISD provides two algorithms: CISD that identifies chromatin interaction sites at kilobase resolution from MNase-seq data and CISD_loop for prediction of CCIs from low-resolution HiC and data. This approach facilitates the expansion of the field of 3D genome research by allowing the exploration of more cell types, tissues and species.


Visualizes next-generation sequencing (NGS) signals and sequence motif densities along genomic features using average plots and heatmaps. It can also calculate sequence motif density profiles from reference genome. SeqPlots is useful both for exploratory data analyses and preparing replicable, publication quality plots. Other features of the software include collaboration and data sharing capabilities, as well as ability to store pre-calculated result matrixes, that combine many sequencing experiments and in-silico generated tracks with multiple different features.


Automates the processing and analysis of several commonly used Next Generation Sequencing (NGS) datasets including: ChIP-seq, RNA-seq, Global Run On sequencing (GRO-seq), micrococcal nuclease footprint sequencing (MNase-seq), DNase hypersensitivity sequencing (DNase-seq), and transposase-accessible chromatin using sequencing ATAC-seq datasets. CIPHER provides an analysis mode that accomplishes complex bioinformatics tasks such as enhancer prediction. It supplies functions to integrate various NGS datasets together.