ggbio protocols

View ggbio computational protocol

ggbio statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Genome visualization Circos plot generation chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

ggbio specifications

Information


Unique identifier OMICS_04660
Name ggbio
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Medium
Version 1.28.5
Stability Stable
Requirements
AnnotationDbi, methods, stats, grid, graphics, BiocGenerics, Biobase, utils, testthat, Biostrings, BiocStyle, grDevices, SummarizedExperiment, BSgenome, BSgenome.Hsapiens.UCSC.hg19, chipseq, GenomicRanges(>=1.29.14), IRanges(>=2.11.16), scales, knitr, reshape2, vsn, EnsDb.Hsapiens.v75, TxDb.Hsapiens.UCSC.hg19.knownGene, OrganismDbi, Hmisc, gridExtra, S4Vectors(>=0.13.13), GenomeInfoDb(>=1.1.3), ggplot2(>=1.0.0), gtable, biovizBase(>=1.28.2), Rsamtools(>=1.17.28), GenomicAlignments(>=1.1.16), VariantAnnotation(>=1.11.4), rtracklayer(>=1.25.16), GenomicFeatures(>=1.29.11), GGally, ensembldb(>=1.99.13), AnnotationFilter, rlang, Homo.sapiens, TxDb.Mmusculus.UCSC.mm9.knownGene, tinytex
Maintained Yes

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline Michael Lawrence <>

Publication for ggbio

ggbio in pipelines

 (4)
2018
PMCID: 5801106
PMID: 29430376
DOI: 10.1007/s13205-018-1140-3

[…] studio® software (ariadne inc., rockville, md, usa). to predict the functions of the selected genes, we identified the most likely chromosomal positions of each gene using the fstval program (ggbio inc., yongin, korea). we found the best mapping position using the blastn tool (https://blast.ncbi.nlm.nih.gov/) with an e value cutoff of ≤ 1.0 × 10−5. we anchored each gene position […]

2015
PMCID: 4572072
PMID: 26025378
DOI: 10.1093/hmg/ddv203

[…] the resulting plots and the data used for plotting. data for plotting are stored in sqlite database which is accessed using r scripts. plots are displayed mainly using rstudio, sqldf, ggplot and ggbio (–). at the time of submission, the application is currently in beta stage for external users, with most functionality in place and performance issues resolved. we are continuously working […]

2013
PMCID: 3570548
PMID: 23424639
DOI: 10.1371/journal.pone.0055895

[…] of the signatures was assessed as described above., heat-maps were generated using the mev program from the tm4 package of microarray tools , and chromosome regions were drawn using the r libraries ggbio and ggplot2 , ., a graphical user interface (gui) driven implementation of the dac was created to simplify the classification process for users. the code behind the gui was written in python […]

2012
PMCID: 3603004
PMID: 23264558
DOI: 10.1093/mp/sss160

[…] × 5,000,000., phased sirna analyses were performed using the ta-sirna prediction tool in the uea srna workbench () with default parameters., the chromosome distribution charts were created using the ggbio tool, an r/bioconductor package ()., dcl family protein sequences were identified by similarity searches at phytozome.net and aligned using the software muscle (). unambiguously aligned regions […]


To access a full list of citations, you will need to upgrade to our premium service.

ggbio in publications

 (37)
PMCID: 5959919
PMID: 29777105
DOI: 10.1038/s41467-018-04256-y

[…] detected in all control and taqed strains were also eliminated as false positives. genome-rearrangement/mutation events are visualized in figs.  and as circular plots generated by the r package (ggbio; https://bioconductor.org/packages/release/bioc/html/ggbio.html)., all illumina reads from control and taqed plants were trimmed using clc genomics workbench (v8.5; qiagen) to a minimum quality […]

PMCID: 5850119
PMID: 29568492
DOI: 10.5256/f1000research.14748.r30355

[…] of genomic locations to genes. while options for the visualisations of genomic data and interactions are outside the scope of this workflow, at least three good alternatives exist in bioconductor: ggbio , sushi and gviz coupled with the genomicinteractions package . we refer the reader to these publications and package vignettes for examples., as the sample size and power of gwass and gene […]

PMCID: 5801106
PMID: 29430376
DOI: 10.1007/s13205-018-1140-3

[…] studio® software (ariadne inc., rockville, md, usa). to predict the functions of the selected genes, we identified the most likely chromosomal positions of each gene using the fstval program (ggbio inc., yongin, korea). we found the best mapping position using the blastn tool (https://blast.ncbi.nlm.nih.gov/) with an e value cutoff of ≤ 1.0 × 10−5. we anchored each gene position […]

PMCID: 5788975
PMID: 29379011
DOI: 10.1038/s41467-017-02706-7

[…] are not falsely identified as integration events. the resulting positive reads were then mapped to the mm10 mouse genome using bwa-mem. integration events were summarized using a custom r-script (ggbio) to display as a karyogram., sequencing data have been deposited in the ncbi sequence read archive (sra) under accession code 127366 . all other data are available from the authors upon […]

PMCID: 5727874
PMID: 29233099
DOI: 10.1186/s12864-017-4364-4

[…] poisson test using the function ppois to compare the percentage of de genes within the window with the percentage of de genes in the entire genome. data were visualized using genomicranges [] and ggbio []., tracks for snp identification and visualization were created using integrative genomics viewer []. identified snps were incorporated into the reference sequences from ensembl, […]


To access a full list of publications, you will need to upgrade to our premium service.

ggbio institution(s)
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA; Department of Statistics, Iowa State University, Ames, IA, USA; Department of Bioinformatics, Genentech, San Francisco, CA, USA
ggbio funding source(s)
Supported by Genentech Research and Early Development, Inc.

ggbio reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review ggbio