Package: karyotapR 1.0.1.9000

karyotapR: DNA Copy Number Analysis for Genome-Wide Tapestri Panels

Analysis of DNA copy number in single cells using custom genome-wide targeted DNA sequencing panels for the Mission Bio Tapestri platform. Users can easily parse, manipulate, and visualize datasets produced from the automated 'Tapestri Pipeline', with support for normalization, clustering, and copy number calling. Functions are also available to deconvolute multiplexed samples by genotype and parsing barcoded reads from exogenous lentiviral constructs.

Authors:Joseph Mays [aut, cre, cph]

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karyotapR.pdf |karyotapR.html✨
karyotapR/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/joeymays/karyotapr/issues

On CRAN:

3.16 score 1 stars 29 scripts 185 downloads 31 exports 92 dependencies

Last updated 9 months agofrom:f675f908c0. Checks:OK: 5 WARNING: 1 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 08 2024
R-4.5-winOKNov 08 2024
R-4.5-linuxWARNINGNov 08 2024
R-4.4-winOKNov 08 2024
R-4.4-macOKNov 08 2024
R-4.3-winOKNov 08 2024
R-4.3-macNOTENov 08 2024

Exports:.TapestriExperimentassayBoxPlotassayHeatmapbarcodeProbebarcodeProbe<-calcCopyNumbercalcGMMCopyNumbercalcNormCountscalcSmoothCopyNumbercallSampleLablescornercountBarcodedReadscountBarcodedReadsFromContigcreateTapestriExperimentgenerateControlCopyNumberTemplategetChrOrdergetCytobandsgetGMMBoundariesgetTidyDatagmmParamsgrnaProbegrnaProbe<-moveNonGenomeProbesnewTapestriExperimentExamplePCAKneePlotplotCopyNumberGMMreducedDimPlotrunClusteringrunPCArunUMAPshow

Dependencies:abindaskpassBiobaseBiocGenericscirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurldbscanDelayedArraydigestdoParalleldplyrfansifarverfitdistrplusforeachgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggplot2GlobalOptionsgluegtablegtoolsherehttrIRangesisobanditeratorsjsonlitelabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigpngpurrrR6rappdirsRColorBrewerRcppRcppEigenRcppTOMLreticulaterhdf5rhdf5filtersRhdf5librjsonrlangrprojrootRSpectraS4ArraysS4VectorsscalesshapeSingleCellExperimentSparseArraystringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectUCSC.utilsumaputf8vctrsviridisLitewithrXVectorzlibbioc

Readme and manuals

Help Manual

Help pageTopics
Generate a box plot from assay dataassayBoxPlot
Generate heatmap of assay dataassayHeatmap
Calculate relative copy number value for each cell-probe unit using reference samplecalcCopyNumber generateControlCopyNumberTemplate
Call copy number for each cell-chromosome using Gaussian mixture modelscalcGMMCopyNumber
Normalize raw countscalcNormCounts
Smooth copy number values across chromosomes and chromosome armscalcSmoothCopyNumber
Call sample labels based on feature countscallSampleLables
Print the top-left corner of a matrixcorner
Get read counts from barcoded readscountBarcodedReads countBarcodedReadsFromContig
Create 'TapestriExperiment' object from Tapestri Pipeline outputcreateTapestriExperiment
Getter and Setter functions for 'TapestriExperiment' slotsbarcodeProbe barcodeProbe,TapestriExperiment-method barcodeProbe<- barcodeProbe<-,TapestriExperiment-method Custom Slot Getters and Setters gmmParams gmmParams,TapestriExperiment-method grnaProbe grnaProbe,TapestriExperiment-method grnaProbe<- grnaProbe<-,TapestriExperiment-method
Get chromosome order from a string of chromosome/contig namesgetChrOrder
Add chromosome cytobands and chromosome arms to 'TapestriExperiment'getCytobands
Calculate decision boundaries between components of copy number GMMsgetGMMBoundaries
Get tidy-style data from 'TapestriExperiment' objectsgetTidyData
Move non-genome probes counts and metadata to altExp slotsmoveNonGenomeProbes
Create Example 'TapestriExperiment'newTapestriExperimentExample
Plot of PCA proportion of variance explainedPCAKneePlot
Plot copy number GMM componentsplotCopyNumberGMM
Scatter plot for dimensional reduction resultsreducedDimPlot
Cluster 2D datarunClustering
Cluster assay data by Principal Components AnalysisrunPCA
Cluster matrix data by UMAPrunUMAP
TapestriExperiment Class Definition.TapestriExperiment show,TapestriExperiment-method TapestriExperiment-class