Package: MADSEQ 1.33.0

Yu Kong

MADSEQ: Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data

The MADSEQ package provides a group of hierarchical Bayeisan models for the detection of mosaic aneuploidy, the inference of the type of aneuploidy and also for the quantification of the fraction of aneuploid cells in the sample.

Authors:Yu Kong, Adam Auton, John Murray Greally

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

# Install 'MADSEQ' in R:

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

Bug tracker:https://github.com/ykong2/madseq/issues

Uses libs:

jags– Just Another Gibbs Sampler for Bayesian MCMC
c++– GNU Standard C++ Library v3

Datasets:

aneuploidy_chr18 - An S4 class MadSeq object

On BioConductor:MADSEQ-1.33.0(bioc 3.21)MADSEQ-1.32.0(bioc 3.20)

genomicvariation somaticmutation variantdetection bayesian copynumbervariation sequencing coverage jags cpp

3.60 score 4 stars 1 scripts 214 downloads 10 exports 99 dependencies

Last updated 4 months agofrom:4a2b4e337c. Checks:2 ERROR, 6 WARNING. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	FAIL	Feb 17 2025
R-4.5-win	WARNING	Feb 17 2025
R-4.5-mac	WARNING	Feb 17 2025
R-4.5-linux	ERROR	Feb 17 2025
R-4.4-win	WARNING	Feb 17 2025
R-4.4-mac	WARNING	Feb 17 2025
R-4.3-win	WARNING	Feb 17 2025
R-4.3-mac	WARNING	Feb 17 2025

Exports:deltaBIC normalizeCoverage plotFraction plotMadSeq plotMixture posterior prepareCoverageGC prepareHetero runMadSeq summary

Dependencies:abind AnnotationDbi ape askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome BSgenome.Hsapiens.UCSC.hg19 cachem cli cluster coda codetools cpp11 crayon curl DBI DelayedArray digest dplyr fansi fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges glue httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise memuse mgcv mime nlme openssl permute pillar pinfsc50 pkgconfig plogr png preprocessCore R6 Rcpp RCurl restfulr Rhtslib rjags rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyselect UCSC.utils utf8 VariantAnnotation vcfR vctrs vegan VGAM viridisLite withr XML XVector yaml zlibbioc

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Mosaic Aneuploidy Detection using Massive Parallel Sequencing Data (MADSEQ)	MADSEQ-package
An S4 class MadSeq object	aneuploidy_chr18
Accessing delta BIC of MadSeq object	deltaBIC deltaBIC,MadSeq-method
The MadSeq class	MadSeq MadSeq-class
correct coverage bias due to GC content	normalizeCoverage
histgram for the fraction of aneuploid cells estimated by MadSeq model	plotFraction plotFraction,MadSeq-method
density plot for posterior distribution of selected model	plotMadSeq plotMadSeq,MadSeq-method
density plot for the posterior distribution of alternative allele frequency estimated from the selected model	plotMixture plotMixture,MadSeq-method
Accessing posterior distribution of MadSeq object	posterior posterior,MadSeq-method
get sequencing coverage and GC content for targeted regions	prepareCoverageGC
prepare heterozygous sites for aneuploidy detection	prepareHetero
Model to detect and quantify mosaic aneuploidy	runMadSeq
Summarize statistics of the MadSeq object	summary summary,MadSeq-method