title: glbase: a framework for combining, analyzing and displaying heterogeneous genomic and high-throughput sequencing data.
abstract: Genomic datasets and the tools to analyze them have proliferated at an astonishing rate. However, such tools are often poorly integrated with each other: each program typically produces its own custom output in a variety of non-standard file formats. Here we present glbase, a framework that uses a flexible set of descriptors that can quickly parse non-binary data files. glbase includes many functions to intersect two lists of data, including operations on genomic interval data and support for the efficient random access to huge genomic data files. Many glbase functions can produce graphical outputs, including scatter plots, heatmaps, boxplots and other common analytical displays of high-throughput data such as RNA-seq, ChIP-seq and microarray expression data. glbase is designed to rapidly bring biological data into a Python-based analytical environment to facilitate analysis and data processing. In summary, glbase is a flexible and multifunctional toolkit that allows the combination and analysis of high-throughput data (especially next-generation sequencing and genome-wide data), and which has been instrumental in the analysis of complex data sets. glbase is freely available at http://bitbucket.org/oaxiom/glbase/.
authors.affiliation: Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530 China.
authors.forename: Andrew Paul
authors.initials: AP
authors.lastname: Hutchins
authors.affiliation: Genome Regulation Laboratory, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530 China ; Laboratory for Structural Biochemistry, Genome Institute of Singapore, 60 Biopolis Street, Singapore, 138672 Singapore.
authors.forename: Ralf
authors.initials: R
authors.lastname: Jauch
authors.affiliation: Laboratory for Structural Biochemistry, Genome Institute of Singapore, 60 Biopolis Street, Singapore, 138672 Singapore ; Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
authors.forename: Mateusz
authors.initials: M
authors.lastname: Dyla
authors.affiliation: Fibrosis Laboratories, Institute of Cellular Medicine, Newcastle University Medical School, Framlington Place, Newcastle upon Tyne, NE2 4HH UK.
authors.forename: Diego
authors.initials: D
authors.lastname: Miranda-Saavedra
keywords: Bioinformatics; ChIP-seq; Genomics; Microarray; Motifs; RNA-seq; Transcription factor