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GenomeGraphs: integrated genomic data visualization with R

Steffen Durinck, James Bullard, Paul T Spellman, Sandrine Dudoit
2009 BMC Bioinformatics  
In addition, genomic data analysis requires integrated visualization of experimental data along with constantly changing genomic annotation and statistical analyses.  ...  We developed GenomeGraphs, as an add-on software package for the statistical programming environment R, to facilitate integrated visualization of genomic datasets.  ...  Grid is typically installed together with the base installation of R.  ... 
doi:10.1186/1471-2105-10-2 pmid:19123956 pmcid:PMC2629762 fatcat:vk4rd4vyy5airap55dckjyysuq

rtracklayer: an R package for interfacing with genome browsers

M. Lawrence, R. Gentleman, V. Carey
2009 Bioinformatics  
ACKNOWLEDGEMENTS We would like to thank Dr Muneesh Tewari for helpful discussions and the gene expression data. Funding: NHGRI (grant P41HG004059 to R.G., in part).  ...  As part of the Bioconductor project, rtracklayer aims to integrate genomic visualizations with experimental data analysis.  ...  Some R/Bioconductor packages already provide genomic visualizations and these include GenomeGraphs (Durinck et al., 2009 ) and xmapbridge.  ... 
doi:10.1093/bioinformatics/btp328 pmid:19468054 pmcid:PMC2705236 fatcat:cljv67pm2femdjntqsdcrschj4

Mapsnp: An R Package to Plot a Genomic Map for Single Nucleotide Polymorphisms

Fuquan Zhang, Yong Xu, Hongbao Cao, Chunhui Jin, Zaohuo Cheng, Guoqiang Wang, Yin Yao Shugart, Jonathan Arthur
2015 PLoS ONE  
mapsnp is a simple and flexible software package which can be used to visualize a genomic map for SNPs, integrating a chromosome ideogram, genomic coordinates, SNP locations and SNP labels.  ...  Therefore, we developed an R package, "mapsnp", to plot genomic map for a panel of SNPs within a genome region of interest, including the relative chromosome location and the transcripts in the region.  ...  There are several programming tools for visualizing genomic data, such as GenomeGraphs [5] , ggbio [6] , and Gviz [7] .  ... 
doi:10.1371/journal.pone.0123609 pmid:25853637 pmcid:PMC4390227 fatcat:zgoiqx2se5hxfnbgrblfw63pxq

chromPlot: visualization of genomic data in chromosomal context [article]

Karen Y Orostica, Ricardo A Verdugo
2015 biorxiv/medrxiv   pre-print
The package is implemented in R so that visualization can be easily integrated with its numerous packages for processing genomic data.  ...  Visualizing genomic data in chromosomal context can help detecting errors in data generation or analysis and can suggest new hypotheses to be tested.  ...  GenomeGraphs (Durinck et al., 2009) and GenoPlotR (Guy et al., 2010) R packages and the Integrative Genomics Viewer (IGV) (Thorvaldsd ottir et al., 2013) .  ... 
doi:10.1101/034108 fatcat:3ptib22fjbdivfqgsflw7q7j6a

genoPlotR: comparative gene and genome visualization in R

L. Guy, J. Roat Kultima, S. G. E. Andersson
2010 Bioinformatics  
The amount of gene and genome data obtained by next-generation sequencing technologies generates a need for comparative visualization tools.  ...  Availability: genoPlotR is a platform-independent R package, available with full source code under a GPL2 license at R-Forge: http://genoplotr.r-forge.r-project.org/ Contact:  ...  GenomeGraphs (Durinck et al., 2009 ) is a R package, which allows the visualization of one genomic region with related datasets such as microarray data.  ... 
doi:10.1093/bioinformatics/btq413 pmid:20624783 pmcid:PMC2935412 fatcat:3aswcnq4tzdkraupo6s4mifeai

Reproducible probe-level analysis of the Affymetrix Exon 1.0 ST array with R/Bioconductor

M. Rodrigo-Domingo, R. Waagepetersen, J. S. Bodker, S. Falgreen, M. K. Kjeldsen, H. E. Johnsen, K. Dybkaer, M. Bogsted
2013 Briefings in Bioinformatics  
We believe this study will provide other researchers with an easy way of accessing gene expression data at different annotation levels and with the sufficient details needed for developing their own tools  ...  Karen Dybk×r is a molecular biologist and senior scientist.  ...  research is supported by MSCNET, a translational program studying cancer stem cells in multiple myeloma supported by the EU FP6, and CHEPRE, a program studying chemo sensitivity in malignant lymphoma by genomic  ... 
doi:10.1093/bib/bbt011 pmid:23603090 pmcid:PMC4103539 fatcat:tsxmdaezjjb7rktbqturv5sfha

Reproducible probe-level analysis of the Affymetrix Exon 1.0 ST array with R/Bioconductor [article]

Maria Rodrigo-Domingo, Rasmus Waagepetersen, Julie Støve Bødker, Steffen Falgreen, Malene Krag Kjeldsen, Hans Erik Johnsen, Karen Dybkær, Martin Bøgsted
2013 arXiv   pre-print
We believe this study will provide other researchers with an easy way of accessing gene expression data at different annotation levels and with the sufficient details needed for developing their own tools  ...  Reproducing results from published microarray data represents a challenge due to the vast amounts of data and the large variety of pre-processing and filtering steps employed before the actual analysis  ...  JSB, MKK, HEJ and KDS assisted with data interpretation and participated in paper drafting. MB conceived and tested the workflow, assisted in manuscript drafting and coordinated the work.  ... 
arXiv:1302.3790v2 fatcat:zsfekoydbfamxbawwb5kggzv64

RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms

Zhaodong Hao, Dekang Lv, Ying Ge, Jisen Shi, Dolf Weijers, Guangchuang Yu, Jinhui Chen
2020 PeerJ Computer Science  
It can map continuous and discrete genome-wide data on the idiograms and visualize them in a heat map and track labels, respectively.  ...  As more and more non-model species are sequenced with chromosome-level assembly being available, tools that can generate idiograms for a broad range of species and be capable of visualizing more data types  ...  Thus, there is a lack of a R package for non-circular genome visualization and allowing to visualize genome-wide relationships between two or more species using Bezier curves on idiograms.  ... 
doi:10.7717/peerj-cs.251 pmid:33816903 pmcid:PMC7924719 fatcat:3l3ouu7vkzakzo6inskbh5rwga

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

Lihua J Zhu, Claude Gazin, Nathan D Lawson, Hervé Pagès, Simon M Lin, David S Lapointe, Michael R Green
2010 BMC Bioinformatics  
statistical programming environment R.  ...  Tight integration to the biomaRt package enables up-to-date annotation retrieval from the BioMart database.  ...  We also thank Zhiping Weng in the Program of Bioinformatics and Integrative Biology at UMMS for reviewing the manuscript, Ivan Gregoretti at National Institute Health for helping with the revision, Sara  ... 
doi:10.1186/1471-2105-11-237 pmid:20459804 pmcid:PMC3098059 fatcat:q23nfrm6yzd43hi5226ds5c66e

GeneProf data: a resource of curated, integrated and reusable high-throughput genomics experiments

Florian Halbritter, Anastasia I. Kousa, Simon R. Tomlinson
2013 Nucleic Acids Research  
GeneProf Data (http://www.geneprof.org) is an open web resource for analysed functional genomics experiments.  ...  GeneProf makes these data instantly accessible in an easily interpretable, searchable and reusable manner and thus opens up the path to the advantages and insights gained from genome-scale experiments  ...  Integrated Genome Browser Genome browsers are powerful and popular tools to visually explore large-scale genomics data sets.  ... 
doi:10.1093/nar/gkt966 pmid:24174536 pmcid:PMC3965072 fatcat:vk4t3z7z25cs3esqemz6kfcbmi

ggbio: an R package for extending the grammar of graphics for genomic data

Tengfei Yin, Dianne Cook, Michael Lawrence
2012 Genome Biology  
We introduce ggbio, a new methodology to visualize and explore genomics annotations and high-throughput data.  ...  The plots provide detailed views of genomic regions, summary views of sequence alignments and splicing patterns, and genome-wide overviews with karyogram, circular and grand linear layouts.  ...  Acknowledgements We are grateful to James Koltes, Kadir Kizilkaya and Jim Reecy for sharing their Angus cattle infectious bovine keratoconjunctivitis data.  ... 
doi:10.1186/gb-2012-13-8-r77 pmid:22937822 pmcid:PMC4053745 fatcat:5ncnqoxsgjdttbowaexapzrxaq

GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments

Ivan Yevshin, Ruslan Sharipov, Tagir Valeev, Alexander Kel, Fedor Kolpakov
2016 Nucleic Acids Research  
genome browser that provides visualization of the GTRD data: read alignments, peaks, clusters, metaclusters and information about gene structures from the Ensembl database and binding sites predicted  ...  browsing and displaying information; (ii) advanced search possibilities, e.g. search of TFBSs near the specified gene or search of all genes potentially regulated by a specified transcription factor; (iii) integrated  ...  It provides powerful possibilities for analyses of highthroughput data with the help of scripting languages (R and JavaScript) and workflows. It also provides a powerful genome browser (18) .  ... 
doi:10.1093/nar/gkw951 pmid:27924024 pmcid:PMC5210645 fatcat:33l6uk5nbvhsddnxktmeloff7m

Bioinformatics tools and database resources for systems genetics analysis in mice--a short review and an evaluation of future needs

C. Durrant, M. A. Swertz, R. Alberts, D. Arends, S. Moller, R. Mott, P. Prins, K. J. van der Velde, R. C. Jansen, K. Schughart
2011 Briefings in Bioinformatics  
To aid future compatibility of software and exchange of already developed software modules, a strong recommendation was made by the group to integrate HAPPY and R/qtl analysis toolboxes, GeneNetwork and  ...  R should be used as the principal computer language for QTL data analysis in all platforms and a 'cloud' should be used for software dissemination to the community.  ...  C.D. and M.A.S. wrote the manuscript and communicated with the other authors who contributed various parts to the final manuscript.  ... 
doi:10.1093/bib/bbr026 pmid:22396485 pmcid:PMC3294237 fatcat:hplbo5ks4fhwtbmtl2louquhg4

Meander: visually exploring the structural variome using space-filling curves

G. A. Pavlopoulos, P. Kumar, A. Sifrim, R. Sakai, M. L. Lin, T. Voet, Y. Moreau, J. Aerts
2013 Nucleic Acids Research  
With Meander, users can explore variations at different levels of resolution and simultaneously compare up to four different individuals against a common reference.  ...  The introduction of next generation sequencing methods in genome studies has made it possible to shift research from a gene-centric approach to a genome wide view.  ...  ACKNOWLEDGEMENTS The authors would like to thank Jun Cao, Joffrey Fitz, Karl J Schmid and Detlef Weigel for the A. thaliana plant data.  ... 
doi:10.1093/nar/gkt254 pmid:23605045 pmcid:PMC3675473 fatcat:lzsloyxqrjbenppqw2ikpojkvu

GATExplorer: Genomic and Transcriptomic Explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs

Alberto Risueño, Celia Fontanillo, Marcel E Dinger, Javier De Las Rivas
2010 BMC Bioinformatics  
Conclusions: GATExplorer is an integrated database that combines genomic/transcriptomic visualization with nucleotide-level probe mapping.  ...  The application integrates data from four major source databases: Ensembl, RNAdb, Affymetrix and GeneAtlas; and it provides the users with a series of files and packages (R CDFs) to analyze particular  ...  Author Details 1 Bioinformatics and Functional Genomics Research Group, Cancer Research Center (CiC-IBMCC, CSIC/USAL), Salamanca, Spain and 2 Institute for Molecular Bioscience, University of Queensland  ... 
doi:10.1186/1471-2105-11-221 pmid:20429936 pmcid:PMC2875241 fatcat:bejkvf2hzbg4rf6u4pyrs73gpi
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