Gviz protocols

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Gviz specifications

Information


Unique identifier OMICS_17191
Name Gviz
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 Advanced
Version 1.24.0
Stability Stable
Requirements
R(>=2.10.0), methods, RColorBrewer, grid, BiocStyle, lattice, BSgenome.Hsapiens.UCSC.hg19, S4Vectors(>=0.9.25), xtable, BiocGenerics(>=0.11.3), GenomeInfoDb(>=1.1.3), Rsamtools(>=1.17.28), GenomicAlignments(>=1.1.16), digest(>=0.6.8), IRanges(>=1.99.18), GenomicRanges(>=1.17.20), XVector(>=0.5.7), rtracklayer(>=1.25.13), biomaRt(>=2.11.0), AnnotationDbi(>=1.27.5), Biobase(>=2.15.3), GenomicFeatures(>=1.17.22), BSgenome(>=1.33.1), Biostrings(>=2.33.11), biovizBase(>=1.13.8), latticeExtra(>=0.6-26), matrixStats(>=0.8.14)
Maintained Yes

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Maintainer


  • person_outline Florian Hahne <>

Publication for Gviz

Gviz in pipelines

 (3)
2018
PMCID: 5753478
PMID: 29298683
DOI: 10.1186/s12864-017-4386-y

[…] fdr < 0.05., ggplot2 (wickham, 2012) and ggrepel (https://cran.r-project.org/web/packages/ggrepel/index.html) r libraries were used for scatterplots. gene model diagrams were generated using the gviz package []. density plots were generated with the lsd package (https://cran.r-project.org/web/packages/lsd/index.html)., linear rna-seq reads were mapped to the c. elegans ce11 annotation using […]

2017
PMCID: 5345719
PMID: 28082325
DOI: 10.1534/g3.116.038190

[…] using fastq-multx (https://github.com/brwnj/fastq-multx), and aligned using bwa as described above. we then inspected read alignments from selected, error-prone markers using the r package gviz (). when we analyzed the 10 f2 individuals that showed the highest number of single heterozygous genotypes flanked on both sides by nipponbare alleles (aha-type error, for more details see […]

2016
PMCID: 5389606
PMID: 27903907
DOI: 10.1093/nar/gkw1178

[…] generated using seqminer () and ngsplot (), using default settings, respectively. all other plots were generated using r (http://www.r-project.org) (). genome browsers snapshots were generated using gviz biocondutor package ()., wildtype s2 cells (120 × 106 cells) were harvested. nuclei were isolated and the immunoprecipitation was carried out as previously described (). the immunoprecipitated […]


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Gviz in publications

 (13)
PMCID: 5958065
PMID: 29773854
DOI: 10.1038/s41598-018-26112-1

[…] were compared to the aforementioned comparison snp set using a 2-sided fisher’s exact test. visualizations highlighting functional annotations of selected 3-snp haplotypes were created with the “gviz” r/bioconductor package., the genetic data analyzed in this study are available in the european genome-phenome archive under study accession number egas00001002915 […]

PMCID: 5863514
PMID: 29599703
DOI: 10.3389/fnins.2018.00119

[…] a value of 0.9. peaks were annotated based on nearest transcription start site (tss) using the bioconductor package chippeakanno (zhu et al., ) and chipseeker (yu et al., ) and visualized using the gviz package (hahne and ivanek, )., the sp8 chipseq data presented in the “results” section were obtained using the goat polyclonal anti-sp8 antibody. these results were confirmed with a sp8 chipseq […]

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

[…] # uncomment the following line to install packages #bioclite(c("clusterprofiler", "deseq2", "genomicfeatures", "genomicinteractions", "genomicranges", "ggplot2", "gviz", "gwascat", "interactionset", "recount", "pheatmap", "rcolorbrewer", "rtracklayer", "r.utils", "splitstackshape", "variantannotation")) , we start with a common scenario: we ran a rna-seq […]

PMCID: 5786503
PMID: 29275859
DOI: 10.1016/j.cell.2017.11.042

[…] coverage tracks of atac signals we created normalized bigwig files using the homer v4.9.1 command makeucscfile with a specified fragment length of the exact read length and used the bioconductor gviz v1.20.0 package for visualization (). chromatin accessibility of degs was inferred by comparing log-transformed mean counts (cpm) of the accessible regions annotated to the respective genes […]

PMCID: 5763571
PMID: 29321036
DOI: 10.1186/s12989-017-0239-8

[…] (logfc) determined the differences between libraries (control, red and maternal nano-tio2 exposed, blue) within the mds plots (fig. ). to visualize read coverage, the r packages chippeakanno and gviz were installed []. complex, differential binding was assessed for both the h3k4me3 (fig. ) and h3k27me3 (fig. ) binding loci. together, these results suggest that the immunoprecipitation […]


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Gviz institution(s)
Novartis Institute for Biomedical Research, Basel, Switzerland; Department of Biomedicine, University of Basel, Basel, Switzerland.

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