1 Overview | 2 Installation and Dependencies | 3 Input Data Format | 4 VegaMC | 5 VegaMC: Run Analysis | 6 Analysis of Gastrointestinal Stromal Tumors (GIST) Dataset
Package: VegaMC 3.51.0
Sandro Morganella
VegaMC: VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer
This package enables the detection of driver chromosomal imbalances including loss of heterozygosity (LOH) from array comparative genomic hybridization (aCGH) data. VegaMC performs a joint segmentation of a dataset and uses a statistical framework to distinguish between driver and passenger mutation. VegaMC has been implemented so that it can be immediately integrated with the output produced by PennCNV tool. In addition, VegaMC produces in output two web pages that allows a rapid navigation between both the detected regions and the altered genes. In the web page that summarizes the altered genes, the link to the respective Ensembl gene web page is reported.
Authors:
VegaMC_3.51.0.tar.gz
VegaMC_3.51.0.zip(r-4.7)VegaMC_3.51.0.zip(r-4.6)VegaMC_3.51.0.zip(r-4.5)
VegaMC_3.51.0.tgz(r-4.6-x86_64)VegaMC_3.51.0.tgz(r-4.6-arm64)VegaMC_3.51.0.tgz(r-4.5-x86_64)VegaMC_3.51.0.tgz(r-4.5-arm64)
VegaMC_3.51.0.tar.gz(r-4.7-arm64)VegaMC_3.51.0.tar.gz(r-4.7-x86_64)VegaMC_3.51.0.tar.gz(r-4.6-arm64)VegaMC_3.51.0.tar.gz(r-4.6-x86_64)
VegaMC_3.51.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
VegaMC/json (API)
| # Install 'VegaMC' in R: |
| install.packages('VegaMC', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:VegaMC-3.51.0(bioc 3.24)VegaMC-3.50.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:42b950b88e. Checks:1 ERROR, 11 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 207 | ||
| linux-devel-arm64 | WARNING | 202 | ||
| linux-devel-x86_64 | WARNING | 243 | ||
| source / vignettes | OK | 240 | ||
| linux-release-arm64 | WARNING | 202 | ||
| linux-release-x86_64 | WARNING | 217 | ||
| macos-release-arm64 | WARNING | 136 | ||
| macos-release-x86_64 | WARNING | 301 | ||
| macos-oldrel-arm64 | WARNING | 97 | ||
| macos-oldrel-x86_64 | WARNING | 337 | ||
| windows-devel | WARNING | 154 | ||
| windows-release | WARNING | 142 | ||
| windows-oldrel | WARNING | 144 | ||
| wasm-release | OK | 137 |
Dependencies:AnnotationDbiaskpassBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrdplyrfastmapfilelockgenericsgluehmshttrhttr2IRangesjsonliteKEGGRESTlifecyclemagrittrmemoisemimeopensslpillarpkgconfigpngprettyunitsprogresspurrrR6rappdirsrlangRSQLiteS4VectorsSeqinfostringistringrsystibbletidyrtidyselectutf8vctrswithrxml2XVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer. | VegaMC-package VegaMC |
| This function sorts a dataset file by the genomic position of the probes. | sortData |
| Class aggregator of VegaMC. | vegaMC vegaMC,character-method vegaMC-methods |
