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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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Versioning
No version available
Documentation
Maintainer
- person_outline Florian Hahne <>
Publication for Gviz
Visualizing Genomic Data Using Gviz and Bioconductor.
Gviz citations
(14)Genome wide haplotype association analysis of primary biliary cholangitis risk in Japanese
[…] 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 […]
SP8 Transcriptional Regulation of Cyclin D1 During Mouse Early Corticogenesis
[…] 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 […]
Using regulatory genomics data to interpret the function of disease variants and prioritise genes from expression studies
[…] # 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 […]
Microbiome Influences Prenatal and Adult Microglia in a Sex Specific Manner
[…] 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 […]
Maternal engineered nanomaterial inhalation during gestation alters the fetal transcriptome
[…] (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 […]
Global accumulation of circRNAs during aging in Caenorhabditis elegans
[…] 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 […]
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