Package: VegaMC 3.43.0

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:S. Morganella and M. Ceccarelli

VegaMC_3.43.0.tar.gz
VegaMC_3.43.0.zip(r-4.5)VegaMC_3.43.0.zip(r-4.4)VegaMC_3.43.0.zip(r-4.3)
VegaMC_3.43.0.tgz(r-4.4-arm64)VegaMC_3.43.0.tgz(r-4.4-x86_64)VegaMC_3.43.0.tgz(r-4.3-arm64)VegaMC_3.43.0.tgz(r-4.3-x86_64)
VegaMC_3.43.0.tar.gz(r-4.5-noble)VegaMC_3.43.0.tar.gz(r-4.4-noble)
VegaMC_3.43.0.tgz(r-4.4-emscripten)VegaMC_3.43.0.tgz(r-4.3-emscripten)
VegaMC.pdf |VegaMC.html✨
VegaMC/json (API)

Peer review:

On BioConductor:VegaMC-3.43.0(bioc 3.20)VegaMC-3.42.0(bioc 3.19)

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

bioconductor-package

2 exports 1.51 score 62 dependencies 2 mentions

Last updated 2 months agofrom:0692c25092

Exports:sortDatavegaMC

Dependencies:AnnotationDbiaskpassBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrdigestdplyrfansifastmapfilelockgenericsGenomeInfoDbGenomeInfoDbDatagluehmshttrhttr2IRangesjsonliteKEGGRESTlifecyclemagrittrmemoisemimeopensslpillarpkgconfigplogrpngprettyunitsprogresspurrrR6rappdirsrlangRSQLiteS4VectorsstringistringrsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrxml2XVectorzlibbioc