inst/staticdocs/README_tmp.md

In dnet: Integrative Analysis of Omics Data in Terms of Network, Evolution and Ontology

An open-source R package for integrative analysis of high-throughput digitised data (eg expression, mutation and replication timing) in terms of network, ontology and evolution

Introduction

dnet intends to analyse the biological network whose nodes/genes are associated with dynamic information such as cross-sample expression levels (mutation status or replication timing), for identifying gene-active dynamic subnetworks.

dnet also supports enrichment analysis using a variety of ontologies (their annotations) and using gene phylostratific age information.

dnet is able to conduct analyses in human but also common model organisms: mouse, rat, chicken, c.elegans, fruitfly, zebrafish and arabidopsis.

dnet aims to deliver a tool with rich visuals but less inputs.

Features

• Identification of gene-active dynamic networks
• Network-based sample classifications and visualisations on 2D sample landscape
• Random walk with restart for network affinity calculation
• Enrichment analysis (Fisher's exact test, Hypergeometric test, Binomial test or KS-like test) that can account for the hierarchy of the ontology
• A wide variety of data supported: ontologies (including Gene Ontology, Disease Ontology, Human Phenotype and Mammalian Phenotype), phylostratific age information and gene association networks in many organisms. For details, please refer to RData.
• This package can run on Windows, Mac and Linux

User I/O

dnet documentation built on Feb. 20, 2020, 3:01 p.m.