Package: CNViz 1.20.0

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_1.20.0.tar.gz
CNViz_1.20.0.zip(r-4.7-any)CNViz_1.20.0.zip(r-4.6-any)CNViz_1.20.0.zip(r-4.5-any)
CNViz_1.20.0.tgz(r-4.6-any)CNViz_1.20.0.tgz(r-4.5-any)
CNViz_1.20.0.tar.gz(r-4.7-any)CNViz_1.20.0.tar.gz(r-4.6-any)
CNViz_1.20.0.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-release.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

3.30 score 1 scripts 1 exports 149 dependencies

Last updated from:6081b50ed4 (on RELEASE_3_23). Checks:8 NOTE, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	NOTE	233
linux-devel-x86_64	NOTE	422
source / vignettes	OK	325
linux-release-x86_64	NOTE	486
macos-release-arm64	NOTE	241
macos-oldrel-arm64	NOTE	261
windows-devel	NOTE	377
windows-release	NOTE	372
windows-oldrel	NOTE	346
wasm-release	OK	214

Exports:launchCNViz

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports bamsignals base64enc bezier BH Biobase BiocGenerics BiocIO biocmake BiocParallel Biostrings biovizBase bit bit64 bitops blob BSgenome bslib cachem checkmate cigarillo cli cluster cn.mops codetools colorspace commonmark CopyNumberPlots cpp11 crayon crosstalk curl data.table DBI DelayedArray dichromat digest dir.expiry dplyr DT ensembldb evaluate farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb 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 Matrix MatrixGenerics matrixStats memoise mime nnet openssl otel pillar pkgconfig 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 S7 sass scales Seqinfo shiny snow sourcetools SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 VariantAnnotation vctrs viridisLite withr xfun XML xtable XVector 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