Package: CNViz 1.21.0

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_1.21.0.tar.gz
CNViz_1.21.0.zip(r-4.7)CNViz_1.21.0.zip(r-4.6)CNViz_1.21.0.zip(r-4.5)
CNViz_1.21.0.tgz(r-4.6-any)CNViz_1.21.0.tgz(r-4.5-any)
CNViz_1.21.0.tar.gz(r-4.7-any)CNViz_1.21.0.tar.gz(r-4.6-any)
CNViz_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CNViz/json (API)

# 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-1.21.0(bioc 3.24)CNViz-1.20.0(bioc 3.23)

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

visualization copynumbervariation sequencing dnaseq

3.48 score 1 scripts 1 exports 75 dependencies

Last updated from:b812289656. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	218
linux-devel-x86_64	NOTE	224
source / vignettes	OK	242
linux-release-x86_64	NOTE	252
macos-release-arm64	NOTE	128
macos-oldrel-arm64	NOTE	108
windows-devel	NOTE	169
windows-release	NOTE	159
windows-oldrel	NOTE	161
wasm-release	OK	199

Exports:launchCNViz

Dependencies:askpass base64enc BiocGenerics bslib cachem cli commonmark cpp11 crosstalk curl data.table digest dplyr DT evaluate farver fastmap fontawesome fs generics GenomicRanges ggplot2 glue gtable highr htmltools htmlwidgets httpuv httr IRanges isoband jquerylib jsonlite knitr labeling later lazyeval lifecycle magrittr memoise mime openssl otel pillar pkgconfig plotly promises purrr R6 rappdirs RColorBrewer Rcpp rlang rmarkdown S4Vectors S7 sass scales Seqinfo shiny sourcetools stringi stringr sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun xtable yaml

CNViz

Rendered fromCNViz.Rmdusingknitr::rmarkdown

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