Package: ACE 1.25.0

Jos B Poell

ACE: Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing

Uses segmented copy number data to estimate tumor cell percentage and produce copy number plots displaying absolute copy numbers.

Authors:Jos B Poell

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

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

Peer review:

Bug tracker:https://github.com/tgac-vumc/ace/issues

Datasets:

On BioConductor:ACE-1.23.0(bioc 3.20)ACE-1.22.0(bioc 3.19)

copynumbervariationdnaseqcoveragewholegenomevisualizationsequencing

5.98 score 14 stars 17 scripts 310 downloads 20 exports 78 dependencies

Last updated 23 days agofrom:0696f37e29. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 30 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 30 2024
R-4.4-macNOTEOct 30 2024
R-4.3-winNOTEOct 30 2024
R-4.3-macNOTEOct 30 2024

Exports:ACEcallanalyzegenomiclocationscompresstemplatecorrelationmatrixcorrelationmatrixadjustedforcesegmentsontemplategetadjustedsegmentslinkvariantsloopsquaremodelobjectsampletotemplateploidyplotlooppostanalysislooprunACEsegmentstotemplatesinglemodelsingleplotsquaremodelsquaremodelsummarytemplatefromequalsegmentstwosamplecompare

Dependencies:askpassBHBiobaseBiocGenericsBiocParallelBiostringsbitopsCGHbaseCGHcallclicodetoolscolorspacecpp11crayoncurldigestDNAcopyfansifarverformatRfutile.loggerfutile.optionsfuturefuture.applyGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2globalsgluegtablehttrimputeIRangesisobandjsonlitelabelinglambda.rlatticelifecyclelimmalistenvmagrittrmarrayMASSMatrixmatrixStatsmgcvmimemunsellnlmeopensslparallellypillarpkgconfigQDNAseqR.methodsS3R.ooR.utilsR6RColorBrewerRhtslibrlangRsamtoolsS4VectorsscalessnowsnowfallstatmodsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

ACE vignette

Jos B. Poell

Rendered fromACE_vignette.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2021-01-15
Started: 2018-05-22

Readme and manuals

Help Manual

Help pageTopics
ACE packageACE-package ACE
Categorize and plot subclonal, single, and double gains / lossesACEcall
Retrieve adjusted copy number information for specific genomic locationsanalyzegenomiclocations
Reduce the size of a template data framecompresstemplate
Segmented data of two tumor samplescopyNumbersSegmented
Create a correlation matrix of all samples in a QDNAseq-objectcorrelationmatrix correlationmatrixadjusted
Custom resegmentation with user-defined segment informationforcesegmentsontemplate
Create a data frame with segment information corresponding to a modelgetadjustedsegments
Append columns with total genomic copies and mutant copies to a file with variant/mutation datalinkvariants
Create 'squaremodel' summaries for all samples in a QDNAseq-objectloopsquaremodel
Converts data of a sample in a QDNAseq-object to a template for ACE functionsobjectsampletotemplate
Batch analysis of samples in a QDNAseq-object for which models have been chosenpostanalysisloop
Absolute Copy number Estimationploidyplotloop runACE
Create a template data frame from input that only provides segment informationsegmentstotemplate
Calculate potential fits for a single samplesinglemodel
Plot an absolute copy number profile for a single samplesingleplot
Calculate potential fits for a single sample using ploidy as a variablesquaremodel
Create a graphical summary of the result of squaremodel fittingsquaremodelsummary
Create a template data frame with artificial segments of equal lengthtemplatefromequalsegments
Overlay copy number data of two samples and compare segment valuestwosamplecompare