Package: CNViz 1.15.0

Rebecca Greenblatt

CNViz: Copy Number Visualization

CNViz takes probe, gene, and segment-level log2 copy number ratios and launches a Shiny app to visualize your sample's copy number profile. You can also integrate loss of heterozygosity (LOH) and single nucleotide variant (SNV) data.

Authors:Rebecca Greenblatt [aut, cre]

CNViz_1.15.0.tar.gz
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CNViz.pdf |CNViz.html✨
CNViz/json (API)
NEWS

# Install 'CNViz' in R:

install.packages('CNViz', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

gene_data - Gene data for vignette example
meta_data - Metadata for vignette example
probe_data - Probe data for vignette example
segment_data - Segment data for vignette example
variant_data - Variant data for vignette example

On BioConductor:CNViz-1.15.0(bioc 3.21)CNViz-1.14.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

visualization copynumbervariation sequencing dnaseq

3.30 score 1 scripts 164 downloads 1 exports 151 dependencies

Last updated 2 months agofrom:5bf989fea4. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 17 2024
R-4.5-win	NOTE	Dec 17 2024
R-4.5-linux	NOTE	Dec 17 2024
R-4.4-win	NOTE	Dec 17 2024
R-4.4-mac	NOTE	Dec 17 2024
R-4.3-win	NOTE	Dec 17 2024
R-4.3-mac	NOTE	Dec 17 2024

Exports:launchCNViz

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports bamsignals base64enc bezier BH Biobase BiocGenerics BiocIO BiocParallel Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate cli cluster cn.mops codetools colorspace commonmark CopyNumberPlots cpp11 crayon crosstalk curl data.table DBI DelayedArray dichromat digest dplyr DT ensembldb evaluate fansi farver fastmap fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gridExtra gtable highr Hmisc htmlTable htmltools htmlwidgets httpuv httr IRanges isoband jquerylib jsonlite karyoploteR KEGGREST knitr labeling lambda.r later lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnet openssl pillar pkgconfig plogr plotly png promises ProtGenerics purrr R6 rappdirs RColorBrewer Rcpp RCurl regioneR restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales shiny snow sourcetools SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite withr xfun XML xtable XVector yaml zlibbioc

CNViz

Rebecca Greenblatt ([email protected])

Rendered fromCNViz.Rmdusingknitr::rmarkdownon Dec 17 2024.

Last update: 2021-05-10
Started: 2021-03-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Data from 2018 TCGA studies from cBioPortal	all_tcga2018_data
Names of 2018 TCGA studies from cBioPortal	cbio_studies
Genomic locations of cytoband labels	cytoband_data
Gene data for vignette example	gene_data
Launches CNViz, a shiny app to visualize your sample's copy number data.	launchCNViz
Metadata for vignette example	meta_data
Probe data for vignette example	probe_data
Segment data for vignette example	segment_data
Variant data for vignette example	variant_data