Scalable genomics with \texttt{R} and bioconductor

DOI10.1214/14-STS476MaRDI QIDQ257684zbMATH OpenOpenAlexWikidataFDO

Authors Michael Lawrence, Martin Morgan

Publication date 17 March 2016

Published in Statistical Science (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1409.2864, https://projecteuclid.org/euclid.ss/1408368572

zbMATH Keywords

\texttt{R}big dataBioconductorbiologygenomics

Mathematics Subject Classification ID

Software, source code, etc. for problems pertaining to statistics (62-04) Graphical methods in statistics (62A09) Software, source code, etc. for problems pertaining to biology (92-04)

Abstract: This paper reviews strategies for solving problems encountered when analyzing large genomic data sets and describes the implementation of those strategies in R by packages from the Bioconductor project. We treat the scalable processing, summarization and visualization of big genomic data. The general ideas are well established and include restrictive queries, compression, iteration and parallel computing. We demonstrate the strategies by applying Bioconductor packages to the detection and analysis of genetic variants from a whole genome sequencing experiment.

Recommendations

• Bioinformatics and computational biology solutions using R and Bioconductor.
• Statistical genomics. Methods and protocols
• Primer to analysis of genomic data using R
• R: An overview and some current directions
• The parallelism motifs of genomic data analysis

Cites work

• Introduction to algorithms
• Software for data analysis. Programming with R
• The plumbing of interactive graphics

Describes a project that uses

Uses Software

• GenomicAlignments
• Biostrings
• VCFtools
• pbdR
• biovizBase
• plumbr
• Samtools
• BatchJobs
• BatchExperiments
• BigWig
• GenomicRanges
• GGobi
• R
• SoDA
• plyr
• Bioconductor
• foreach

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