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Convenience Functions for Biscuit

Bioconductor version: Release (3.19)

A test harness for bsseq loading of Biscuit output, summarization of WGBS data over defined regions and in mappable samples, with or without imputation, dropping of mostly-NA rows, age estimates, etc.

Author: Tim Triche [aut], Wanding Zhou [aut], Benjamin Johnson [aut], Jacob Morrison [aut, cre], Lyong Heo [aut], James Eapen [aut]

Maintainer: Jacob Morrison <jacob.morrison at>

Citation (from within R, enter citation("biscuiteer")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Biscuiteer User Guide HTML R Script
Reference Manual PDF


biocViews DNAMethylation, DataImport, MethylSeq, Software
Version 1.18.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License GPL-3
Depends R (>= 4.1.0), biscuiteerData, bsseq
Imports readr, qualV, Matrix, impute, HDF5Array, S4Vectors, Rsamtools, data.table, Biobase, GenomicRanges, IRanges, BiocGenerics, VariantAnnotation, DelayedMatrixStats, SummarizedExperiment, GenomeInfoDb, Mus.musculus, Homo.sapiens, matrixStats, rtracklayer, QDNAseq, dmrseq, methods, utils, R.utils, gtools, BiocParallel
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Suggests DSS, covr, knitr, rmarkdown, markdown, rlang, scmeth, pkgdown, roxygen2, testthat, QDNAseq.hg19, QDNAseq.mm10, BiocStyle
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Follow Installation instructions to use this package in your R session.

Source Package biscuiteer_1.18.0.tar.gz
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macOS Binary (x86_64) biscuiteer_1.18.0.tgz
macOS Binary (arm64) biscuiteer_1.18.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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