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Title: 3 Quick-Start | CopyKit User Guide

Open Graph Title: 3 Quick-Start | CopyKit User Guide

X Title: 3 Quick-Start | CopyKit User Guide

Description: This is a user guide for the package CopyKit: A toolkit for single-cell CNA analysis.

Open Graph Description: This is a user guide for the package CopyKit: A toolkit for single-cell CNA analysis.

X Description: This is a user guide for the package CopyKit: A toolkit for single-cell CNA analysis.

Generator: bookdown 0.26 and GitBook 2.6.7

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Domain: navinlabcode.github.io

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authorDarlan Conterno Minussi
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Links:

https://navinlabcode.github.io/CopyKit-UserGuide/
1 Introductionhttps://navinlabcode.github.io/CopyKit-UserGuide/index.html
2 Parallelizationhttps://navinlabcode.github.io/CopyKit-UserGuide/parallelization.html
3 Quick-Starthttps://navinlabcode.github.io/CopyKit-UserGuide/quick-start.html
4 Pre-processinghttps://navinlabcode.github.io/CopyKit-UserGuide/pre-processing.html
4.1 From Single Cell BAM fileshttps://navinlabcode.github.io/CopyKit-UserGuide/pre-processing.html#from-single-cell-bam-files
4.1.1 runVarbin()https://navinlabcode.github.io/CopyKit-UserGuide/pre-processing.html#runvarbin
4.2 runVarbin() moduleshttps://navinlabcode.github.io/CopyKit-UserGuide/pre-processing.html#runvarbin-modules
4.3 From external count data or user-defined scaffoldshttps://navinlabcode.github.io/CopyKit-UserGuide/pre-processing.html#from-external-count-data-or-user-defined-scaffolds
5 QC modulehttps://navinlabcode.github.io/CopyKit-UserGuide/qc-module.html
5.1 runMetrics()https://navinlabcode.github.io/CopyKit-UserGuide/qc-module.html#runmetrics
5.2 findAneuploidCells()https://navinlabcode.github.io/CopyKit-UserGuide/qc-module.html#findaneuploidcells
5.3 findOutliers()https://navinlabcode.github.io/CopyKit-UserGuide/qc-module.html#findoutliers
6 kNN smoothinghttps://navinlabcode.github.io/CopyKit-UserGuide/knn-smoothing.html
7 Analysis and Visualization modulehttps://navinlabcode.github.io/CopyKit-UserGuide/analysis-and-visualization-module.html
7.1 plotMetrics()https://navinlabcode.github.io/CopyKit-UserGuide/analysis-and-visualization-module.html#plotmetrics
7.2 plotRatio()https://navinlabcode.github.io/CopyKit-UserGuide/analysis-and-visualization-module.html#plotratio
7.3 runUmap()https://navinlabcode.github.io/CopyKit-UserGuide/analysis-and-visualization-module.html#runumap
7.4 scquantum & calcInteger()https://navinlabcode.github.io/CopyKit-UserGuide/analysis-and-visualization-module.html#scquantum-calcinteger
7.5 Clusteringhttps://navinlabcode.github.io/CopyKit-UserGuide/analysis-and-visualization-module.html#clustering
7.5.1 findSugestedK()https://navinlabcode.github.io/CopyKit-UserGuide/analysis-and-visualization-module.html#findsugestedk
7.5.2 findClusters()https://navinlabcode.github.io/CopyKit-UserGuide/analysis-and-visualization-module.html#findclusters
7.5.3 plotUmap()https://navinlabcode.github.io/CopyKit-UserGuide/analysis-and-visualization-module.html#plotumap
7.6 runPca()https://navinlabcode.github.io/CopyKit-UserGuide/analysis-and-visualization-module.html#runpca
7.7 plotHeatmap()https://navinlabcode.github.io/CopyKit-UserGuide/analysis-and-visualization-module.html#plotheatmap
7.8 runPhylo() & plotPhylo()https://navinlabcode.github.io/CopyKit-UserGuide/analysis-and-visualization-module.html#runphylo-plotphylo
7.9 calcConsensus()https://navinlabcode.github.io/CopyKit-UserGuide/analysis-and-visualization-module.html#calcconsensus
7.10 plotConsensusLine()https://navinlabcode.github.io/CopyKit-UserGuide/analysis-and-visualization-module.html#plotconsensusline
7.11 plotGeneCopy()https://navinlabcode.github.io/CopyKit-UserGuide/analysis-and-visualization-module.html#plotgenecopy
7.12 plotFreq()https://navinlabcode.github.io/CopyKit-UserGuide/analysis-and-visualization-module.html#plotfreq
7.13 plotAlluvial()https://navinlabcode.github.io/CopyKit-UserGuide/analysis-and-visualization-module.html#plotalluvial
8 Merging CopyKit Objectshttps://navinlabcode.github.io/CopyKit-UserGuide/merging-copykit-objects.html
9 Session Infohttps://navinlabcode.github.io/CopyKit-UserGuide/session-info.html
10 FAQhttps://navinlabcode.github.io/CopyKit-UserGuide/faq.html
10.1 Error unable to load package after installation.https://navinlabcode.github.io/CopyKit-UserGuide/faq.html#error-unable-to-load-package-after-installation.
10.2 CopyKit is very slow despite parallel processinghttps://navinlabcode.github.io/CopyKit-UserGuide/faq.html#copykit-is-very-slow-despite-parallel-processing
11 Learn morehttps://navinlabcode.github.io/CopyKit-UserGuide/learn-more.html
11.1 Copy Number data from short reads sequencinghttps://navinlabcode.github.io/CopyKit-UserGuide/learn-more.html#copy-number-data-from-short-reads-sequencing
11.2 Principlehttps://navinlabcode.github.io/CopyKit-UserGuide/learn-more.html#principle-lm
11.3 VarBinhttps://navinlabcode.github.io/CopyKit-UserGuide/learn-more.html#varbin-lm
11.4 GC correctionhttps://navinlabcode.github.io/CopyKit-UserGuide/learn-more.html#gccor-lm
11.5 Merge Levelshttps://navinlabcode.github.io/CopyKit-UserGuide/learn-more.html#mergelevels-lm
11.6 How do we infer copy numbershttps://navinlabcode.github.io/CopyKit-UserGuide/learn-more.html#infercn-lm
11.7 Segmentationhttps://navinlabcode.github.io/CopyKit-UserGuide/learn-more.html#segmentation-lm
11.7.1 CBShttps://navinlabcode.github.io/CopyKit-UserGuide/learn-more.html#cbs-lm
Published with bookdownhttps://github.com/rstudio/bookdown
CopyKit User Guidehttps://navinlabcode.github.io/CopyKit-UserGuide/
https://navinlabcode.github.io/CopyKit-UserGuide/quick-start.html#quick-start
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https://navinlabcode.github.io/CopyKit-UserGuide/parallelization.html
https://navinlabcode.github.io/CopyKit-UserGuide/pre-processing.html

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