Package: CNVScope 3.7.3

James Dalgleish

CNVScope: A Versatile Toolkit for Copy Number Variation Relationship Data Analysis and Visualization

Provides the ability to create interaction maps, discover CNV map domains (edges), gene annotate interactions, and create interactive visualizations of these CNV interaction maps.

Authors:James Dalgeish, Yonghong Wang, Jack Zhu, Paul Meltzer

CNVScope_3.7.3.tar.gz
CNVScope_3.7.3.zip(r-4.5)CNVScope_3.7.3.zip(r-4.4)CNVScope_3.7.3.zip(r-4.3)
CNVScope_3.7.3.tgz(r-4.4-any)CNVScope_3.7.3.tgz(r-4.3-any)
CNVScope_3.7.3.tar.gz(r-4.5-noble)CNVScope_3.7.3.tar.gz(r-4.4-noble)
CNVScope_3.7.3.tgz(r-4.4-emscripten)CNVScope_3.7.3.tgz(r-4.3-emscripten)
CNVScope.pdf |CNVScope.html✨
CNVScope/json (API)
NEWS

# Install 'CNVScope' in R:
install.packages('CNVScope', repos = c('https://jamesdalg.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/jamesdalg/cnvscope/issues

Datasets:

On CRAN:

5.58 score 8 stars 24 scripts 381 downloads 26 exports 168 dependencies

Last updated 2 years agofrom:9b6915de7a. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 11 2024
R-4.5-winNOTENov 11 2024
R-4.5-linuxNOTENov 11 2024
R-4.4-winNOTENov 11 2024
R-4.4-macNOTENov 11 2024
R-4.3-winNOTENov 11 2024
R-4.3-macNOTEOct 12 2024

Exports:averageMatrixEdgescalcCNVKernelProbDistcalcVecLMsCNVScopeservercreateChromosomalMatrixSetdivisorsdownsample_genomic_matrixextractNegLogPvalformSampleMatrixFromRawGDCDatafreadGDCfilegetAnnotationMatrixgetAsymmetricBlockIndicesgetBlockAverageMatrixFromBreakpointsgetGlobalRescalingStatsgetInterchromosomalInteractivePlotGRanges_to_underscored_posimportBreakpointBedmatheadpostProcessLinRegMatrixrebinGenomicInteractionsrunCNVScopeLocalrunCNVScopeShinysignedRescaleunderscored_pos_to_GRangeswriteAsymmetricMeltedChromosomalMatrixToDiskwriteMeltedChromosomalMatrixToDisk

Dependencies:abindacnrAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecliclustercodetoolscolorspacecommonmarkcpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestDNAcopydoParalleldplyrensembldbevaluatefansifarverfastmapfilelockfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicInteractionsGenomicRangesggplot2gluegridExtragtableGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvhttrhttr2igraphInteractionSetinterpIRangesisobanditeratorsjointsegjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetOpenImageRopensslpillarpkgconfigplogrplyrpngprettyunitsprogresspromisesProtGenericspurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRCurlreshape2restfulrRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalesshinysnowsourcetoolsSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttifftinytexUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLxml2xtableXVectoryamlzlibbioc

Additional Visualization Examples

Rendered fromadditonal_examples.Rmdusingknitr::rmarkdownon Nov 11 2024.

Last update: 2021-01-04
Started: 2019-07-18

Creating the TARGET Input matrix from public data

Rendered fromcreate_input_matrix.Rmdusingknitr::rmarkdownon Nov 11 2024.

Last update: 2020-07-02
Started: 2018-08-01

Creating Linear Regression Matrices from Segment Data

James Dalgleish

Rendered fromcreate_output_matrix.Rmdusingknitr::rmarkdownon Nov 11 2024.

Last update: 2021-01-04
Started: 2018-08-01

Power Analysis

Rendered frompower_analysis.Rmdusingknitr::rmarkdownon Nov 11 2024.

Last update: 2021-01-04
Started: 2019-07-18

Readme and manuals

Help Manual

Help pageTopics
Average edges of a matrix to facilitate downsampling.averageMatrixEdges
Calculate the probability distribution of CNV concordance events with a fast kernelcalcCNVKernelProbDist
Create a linear regression matrix.calcVecLMs
Server component of the CNVScope plotly shiny application.CNVScopeserver
Create chromosomal interaction matrices for CNVScope shiny application.createChromosomalMatrixSet
List of Divisorsdivisors
Rescale positive and negative data, preserving sign information.downsample_genomic_matrix
Find the negative log p-value of a pair of vectors.extractNegLogPval
Form sample matrix from GDC copy number data files.formSampleMatrixFromRawGDCData
Read GDC segmentation datafile for low-pass sequencing data.freadGDCfile
Get the genes in the genomic ranges indicated by the row and column labels.getAnnotationMatrix
Get Block Indices from an asymmetric (or symmetric) matrix.getAsymmetricBlockIndices
Calculate block averages and areas in a matrix given breakpoints.getBlockAverageMatrixFromBreakpoints
Calculate several base statistics for color rescaling.getGlobalRescalingStats
Create an HTML widget for use in shiny or webshot for a given pair of chromosomes.getInterchromosomalInteractivePlot
Convert GRanges object to underscord positions.GRanges_to_underscored_pos
Import a breakpoint BED file.importBreakpointBed
Gets a small piece of a matrix (top left corner) for viewing, rather than pulling the first n rows.mathead
Neuroblastoma sample CNV relationship matrixnbl_result_matrix_sign_small
Postprocess linear regression matrix.postProcessLinRegMatrix
Assign GenomicInteractions to a predefined series of bins for row and column, corresponding to a genomic matrix.rebinGenomicInteractions
Runs the CNVScope plotly shiny application.runCNVScopeLocal
Runs the CNVScope plotly shiny application.runCNVScopeShiny
Rescale positive and negative data, preserving sign information.signedRescale
Convert coordinates in underscored format to a GRanges object.underscored_pos_to_GRanges
Write a matrix, with genes, of a submatrix of a whole genome interaction matrix to disk.writeAsymmetricMeltedChromosomalMatrixToDisk
Write a matrix, with genes, of a submatrix of a whole genome interaction matrix to disk.writeMeltedChromosomalMatrixToDisk