Biomedical subjects

Roy Storey

Publications and source records attributed to Roy Storey.

4 recordsLinked to original sources

PubMed2026

moiraine: an R package to construct reproducible pipelines for the application and comparison of multi-omics integration methods.

MOTIVATION: In the past decades, many statistical methods for integrating multi-omics data have been developed. They have been implemented into software tools, which differ widely in their programming choices, such as the format required for data input, or the format of the generated integration results. This lack of standards renders cumbersome and time-intensive the application and comparison of different integration tools to the same multi-omics dataset. RESULTS: We have developed the moiraine R package for constructing reproducible multi-omics integration pipelines, which enables users to apply one or more statistical methods for multi-omics integration to their own multi-omics dataset. moiraine facilitates the preprocessing of the omics datasets and automates their formatting for the integration step. It simplifies the interpretation and evaluation of the integration results through the construction of visualizations in which metadata about samples and features can easily be included. Crucially, it enables the comparison of results obtained with different integration tools, allowing users to assess the robustness of their results. AVAILABILITY AND IMPLEMENTATION: The moiraine R package is publicly available at https://github.com/Plant-Food-Research-Open/moiraine; an archival snapshot of the package is available on Zenodo at https://doi.org/10.5281/zenodo.17172718. A detailed tutorial is available at https://plant-food-research-open.github.io/moiraine-manual/.

Software↗

PubMed2006

GENCODE: producing a reference annotation for ENCODE.

BACKGROUND: The GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. This was achieved by a combination of initial manual annotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results. RESULTS: The GENCODE gene features are divided into eight different categories of which only the first two (known and novel coding sequence) are confidently predicted to be protein-coding genes. 5' rapid amplification of cDNA ends (RACE) and RT-PCR were used to experimentally verify the initial annotation. Of the 420 coding loci tested, 229 RACE products have been sequenced. They supported 5' extensions of 30 loci and new splice variants in 50 loci. In addition, 46 loci without evidence for a coding sequence were validated, consisting of 31 novel and 15 putative transcripts. We assessed the comprehensiveness of the GENCODE annotation by attempting to validate all the predicted exon boundaries outside the GENCODE annotation. Out of 1,215 tested in a subset of the ENCODE regions, 14 novel exon pairs were validated, only two of them in intergenic regions. CONCLUSION: In total, 487 loci, of which 434 are coding, have been annotated as part of the GENCODE reference set available from the UCSC browser. Comparison of GENCODE annotation with RefSeq and ENSEMBL show only 40% of GENCODE exons are contained within the two sets, which is a reflection of the high number of alternative splice forms with unique exons annotated. Over 50% of coding loci have been experimentally verified by 5' RACE for EGASP and the GENCODE collaboration is continuing to refine its annotation of 1% human genome with the aid of experimental validation.

Chromosome Mapping↗

PubMed2004

An overview of Ensembl.

Ensembl (http://www.ensembl.org/) is a bioinformatics project to organize biological information around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of individual genomes, and of the synteny and orthology relationships between them. It is also a framework for integration of any biological data that can be mapped onto features derived from the genomic sequence. Ensembl is available as an interactive Web site, a set of flat files, and as a complete, portable open source software system for handling genomes. All data are provided without restriction, and code is freely available. Ensembl's aims are to continue to "widen" this biological integration to include other model organisms relevant to understanding human biology as they become available; to "deepen" this integration to provide an ever more seamless linkage between equivalent components in different species; and to provide further classification of functional elements in the genome that have been previously elusive.

Computational Biology↗

PubMed2004

The Ensembl analysis pipeline.

The Ensembl pipeline is an extension to the Ensembl system which allows automated annotation of genomic sequence. The software comprises two parts. First, there is a set of Perl modules ("Runnables" and "RunnableDBs") which are 'wrappers' for a variety of commonly used analysis tools. These retrieve sequence data from a relational database, run the analysis, and write the results back to the database. They inherit from a common interface, which simplifies the writing of new wrapper modules. On top of this sits a job submission system (the "RuleManager") which allows efficient and reliable submission of large numbers of jobs to a compute farm. Here we describe the fundamental software components of the pipeline, and we also highlight some features of the Sanger installation which were necessary to enable the pipeline to scale to whole-genome analysis.

Base Sequence↗