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ggbio specifications

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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

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Maintainer


  • person_outline Michael Lawrence

Publication for ggbio

ggbio citations

 (37)
library_books

Phenotypic diversification by enhanced genome restructuring after induction of multiple DNA double strand breaks

2018
Nat Commun
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 […]

library_books

Using regulatory genomics data to interpret the function of disease variants and prioritise genes from expression studies

2018
F1000Res
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 […]

library_books

Whole genome resequencing and transcriptomic analysis of genes regulating anthocyanin biosynthesis in black rice plants

2018
3 Biotech
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 […]

library_books

Streamlined ex vivo and in vivo genome editing in mouse embryos using recombinant adeno associated viruses

2018
Nat Commun
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 […]

library_books

Pronounced strain specific chemosensory receptor gene expression in the mouse vomeronasal organ

2017
BMC Genomics
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, […]

library_books

Insights into beta cell regeneration for diabetes via integration of molecular landscapes in human insulinomas

2017
Nat Commun
PMCID: 5626682
PMID: 28974674
DOI: 10.1038/s41467-017-00992-9

[…] normal, with that of beta cell controls slightly more skewed than insulinoma. all features were annotated by snpeff 3.0 using dbsnp version 138 and grch38, ensembl version 78 and visualized using ggbio, granges and ggplot2 within r, ., a signed wgcna algorithm, was used to build co-expression networks, with the log2 of cpm values (after effective library size normalization) as input., […]


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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.

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