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SUMMARY The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters. Four(More)
UNLABELLED ChIPseeker is an R package for annotating ChIP-seq data analysis. It supports annotating ChIP peaks and provides functions to visualize ChIP peaks coverage over chromosomes and profiles of peaks binding to TSS regions. Comparison of ChIP peak profiles and annotation are also supported. Moreover, it supports evaluating significant overlap among(More)
SUMMARY Disease ontology (DO) annotates human genes in the context of disease. DO is important annotation in translating molecular findings from high-throughput data to clinical relevance. DOSE is an R package providing semantic similarity computations among DO terms and genes which allows biologists to explore the similarities of diseases and of gene(More)
The influenza virus (IV) triggers a series of signalling events inside host cells and induces complex cellular responses. Studies have suggested that host factors play an essential role in IV replication. MicroRNAs (miRNAs) represent a class of small non-coding RNAs that target mRNAs, triggering either translation repression or RNA degradation. Emerging(More)
miRNAs are a class of small RNAs that regulate gene expression via RNA silencing machinery. Some viruses also encode miRNAs, contributing to the complex virus-host interactions. A better understanding of viral miRNA functions would be useful in designing new preventive strategies for treating diseases induced by viruses. To meet the challenge for how(More)
Recent advances in high-throughput technologies dramatically increase biological data generation. However, many research groups lack computing facilities and specialists. This is an obstacle that remains to be addressed. Here, we present a Linux distribution, LXtoo, to provide a flexible computing platform for bioinformatics analysis. Unlike most of the(More)
Semantic technology plays a key role in various domains, from conversation understanding to algorithm analysis. As the most efficient semantic tool, ontology can represent, process and manage the widespread knowledge. Nowadays, many researchers use ontology to collect and organize data's semantic information in order to maximize research productivity. In(More)
Description MSnbase provides classes, methods and functions for visualisation, manipulation and processing of mass spectrometry data. Important class are "MSnExp" (raw data file), "MSnSet" (quantitation data) and "ReporterIons" (reporter ions for labelled proteomics). Other classes are "Spectrum" and the subclasses "Spectrum1" (for MS spectra) and(More)