Package: AneuFinder 1.35.0

Aaron Taudt

AneuFinder: Analysis of Copy Number Variation in Single-Cell-Sequencing Data

AneuFinder implements functions for copy-number detection, breakpoint detection, and karyotype and heterogeneity analysis in single-cell whole genome sequencing and strand-seq data.

Authors:Aaron Taudt, Bjorn Bakker, David Porubsky

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

# Install 'AneuFinder' in R:

install.packages('AneuFinder', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ataudt/aneufinder/issues

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:AneuFinder-1.35.0(bioc 3.21)AneuFinder-1.34.0(bioc 3.20)

immunooncology software sequencing singlecell copynumbervariation genomicvariation hiddenmarkovmodel wholegenome cpp

7.70 score 17 stars 37 scripts 424 downloads 16 mentions 37 exports 84 dependencies

Last updated 2 months agofrom:42b78371c8. Checks:OK: 1 NOTE: 5 WARNING: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 30 2024
R-4.5-win-x86_64	WARNING	Oct 31 2024
R-4.5-linux-x86_64	NOTE	Oct 31 2024
R-4.4-win-x86_64	NOTE	Nov 30 2024
R-4.4-mac-x86_64	NOTE	Nov 30 2024
R-4.3-win-x86_64	NOTE	Nov 30 2024
R-4.3-mac-x86_64	NOTE	Nov 30 2024

Exports:Aneufinder bam2GRanges bed2GRanges binReads blacklist breakpointColors clusterByQuality clusterHMMs collapseBins compareMethods consensusSegments correctGC exportCNVs exportGRanges exportReadCounts filterSegments findCNVs findCNVs.strandseq findHotspots fixedWidthBins getBreakpoints getQC getSCEcoordinates heatmapAneuploidies heatmapGenomewide heatmapGenomewideClusters importBed karyotypeMeasures loadFromFiles plot_pca plotHeterogeneity refineBreakpoints simulateReads stateColors strandColors subsetByCNVprofile variableWidthBins

Dependencies:abind AneuFinderData askpass bamsignals BH Biobase BiocGenerics BiocParallel Biostrings bitops cli codetools colorspace cowplot cpp11 crayon curl DelayedArray DNAcopy doParallel ecp fansi farver foreach formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges ggdendro ggplot2 ggrepel glue gtable httr IRanges isoband iterators jsonlite labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mclust mgcv mime munsell nlme openssl pillar pkgconfig plyr R6 RColorBrewer Rcpp reshape2 Rhtslib rlang Rsamtools S4Arrays S4Vectors scales snow SparseArray stringi stringr SummarizedExperiment sys tibble UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

A quick introduction to AneuFinder

Rendered fromAneuFinder.Rnwusingknitr::knitron Nov 30 2024.

Last update: 2020-03-17
Started: 2016-03-07

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Copy-number detection in WGSCS and Strand-Seq data	AneuFinder-package AneuFinder
Bivariate Hidden Markov Model	aneuBiHMM
Wrapper function for the 'AneuFinder' package	Aneufinder
Hidden Markov Model	aneuHMM
Annotate breakpoints	annotateBreakpoints
Import BAM file into GRanges	bam2GRanges
Import BED file into GRanges	bed2GRanges
Find copy number variations (edivisive, bivariate)	bi.edivisive.findCNVs
Find copy number variations (DNAcopy, bivariate)	biDNAcopy.findCNVs
Find copy number variations (bivariate)	biHMM.findCNVs
Binned read counts	binned.data
Bin the genome	binning
Convert aligned reads from various file formats into read counts in equidistant bins	binReads
Make a blacklist for genomic regions	blacklist
Cluster based on quality variables	clusterByQuality
Cluster objects	clusterHMMs
Collapse consecutive bins	collapseBins
'AneuFinder' color scheme	breakpointColors colors stateColors strandColors
Compare copy number calling methods	compareMethods
Compare copy number models	compareModels
Make consensus segments	consensusSegments
GC correction	correctGC
Find copy number variations (DNAcopy, univariate)	DNAcopy.findCNVs
Find copy number variations (edivisive, univariate)	edivisive.findCNVs
Estimate library complexity	estimateComplexity
Export genome browser viewable files	export exportCNVs exportGRanges exportReadCounts
Filter segments by minimal size	filterSegments
Find copy number variations	findCNVs
Find copy number variations (strandseq)	findCNVs.strandseq
Find breakpoint hotspots	findHotspots
Make fixed-width bins	fixedWidthBins
Extract breakpoints	getBreakpoints
Get distinct colors	getDistinctColors
Obtain a data.frame with quality metrics	getQC
Get SCE coordinates	getSCEcoordinates
Plot aneuploidy state	heatmapAneuploidies
Genome wide heatmap of CNV-state	heatmapGenomewide
Plot heatmaps for quality control	heatmapGenomewideClusters
Find copy number variations (univariate)	HMM.findCNVs
Find hotspots of genomic events	hotspotter
Find hotspots of genomic events	hotspotter.variable
Read bed-file into GRanges	importBed
Initialize state factor levels and distributions	initializeStates
Measures for Karyotype Heterogeneity	karyotypeMeasures
Load 'AneuFinder' objects from file	loadFromFiles
Merge Strand-seq libraries	mergeStrandseqFiles
Perform a PCA for copy number profiles	plot_pca
Plotting function for 'aneuBiHMM' objects	plot.aneuBiHMM
Plotting function for 'aneuHMM' objects	plot.aneuHMM
Plotting function for saved 'AneuFinder' objects	plot.character
Plotting function for binned read counts	plot.GRanges
Plotting function for binned read counts (list)	plot.GRangesList
Heterogeneity vs. Aneuploidy	plotHeterogeneity
Plot a histogram of binned read counts with fitted mixture distribution	plotHistogram
Karyogram-like chromosome overview	plotKaryogram
Read count and CNV profile	plotProfile
Print aneuBiHMM object	print.aneuBiHMM
Print aneuHMM object	print.aneuHMM
Quality control measures for binned read counts	qc.bhattacharyya qc.entropy qc.sos qc.spikiness qualityControl
Read AneuFinder configuration file	readConfig
Refine breakpoints	refineBreakpoints
Simulate reads from genome	simulateReads
Get IDs of a subset of models	subsetByCNVprofile
Transform genomic coordinates	transCoord
Make variable-width bins	variableWidthBins
Write AneuFinder configuration file	writeConfig
The Zero-inflated Negative Binomial Distribution	dzinbinom pzinbinom qzinbinom rzinbinom zinbinom