Package: biscuiteer 1.19.0

Jacob Morrison

biscuiteer: Convenience Functions for Biscuit

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.

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

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biscuiteer.pdf |biscuiteer.html✨
biscuiteer/json (API)

# Install 'biscuiteer' in R:

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

Bug tracker:https://github.com/trichelab/biscuiteer/issues

Datasets:

ENSR_subset.hg19 - ENSR_subset data from hg19 genome
ENSR_subset.hg38 - ENSR_subset data from hg38 genome
GRCh37.chromArm - GRCh37.chromArm
GRCh38.chromArm - GRCh38.chromArm
H9state23unmeth.hg19 - H9state23unmeth.hg19
H9state23unmeth.hg38 - H9state23unmeth.hg38
HMM_CpG_islands.hg19 - HMM_CpG_islands.hg19
HMM_CpG_islands.hg38 - HMM_CpG_islands.hg38
clocks - Clocks
hg19.chromArm - Hg19.chromArm
hg38.chromArm - Hg38.chromArm
seqinfo.hg19 - Seqinfo.hg19
seqinfo.hg38 - Seqinfo.hg38
seqinfo.mm10 - Seqinfo.mm10

On BioConductor:biscuiteer-1.19.0(bioc 3.20)biscuiteer-1.18.0(bioc 3.19)

bioconductor-package

33 exports 1.38 score 170 dependencies 1 mentions

Last updated 2 months agofrom:acd4f5dcc4

Exports:atRegions binCoverage biscuitMetadata byChromArm byExtremality checkBiscuitBED condenseSampleNames extremality fexpit filterLoci fixAge fixed fixNAs flogit geno getClock getLogitFracMeth grToSeg header info makeBSseq meta readBiscuit readEpibed RRBSeq samples segToGr simplifySampleNames summarizeBsSeqOver tabixRetrieve unionize WGBSage WGBSeq

Dependencies:abind AnnotationDbi AnnotationHub annotatr askpass beachmat BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocVersion biomaRt Biostrings biscuiteerData bit bit64 bitops blob BSgenome bsseq bumphunter cachem CGHbase CGHcall cli clipr codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray DelayedMatrixStats digest dmrseq DNAcopy doRNG dplyr ExperimentHub fansi farver fastmap filelock foreach formatR futile.logger futile.options future future.apply generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 globals glue GO.db graph gtable gtools HDF5Array hms Homo.sapiens httr httr2 impute IRanges isoband iterators jsonlite KEGGREST KernSmooth labeling lambda.r lattice lifecycle limma listenv locfit magrittr marray MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell Mus.musculus nlme openssl org.Hs.eg.db org.Mm.eg.db OrganismDbi outliers parallelly permute pillar pkgconfig plogr plyr png prettyunits progress purrr QDNAseq qualV R.methodsS3 R.oo R.utils R6 rappdirs RBGL RColorBrewer Rcpp RCurl readr regioneR reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rngtools Rsamtools RSQLite rtracklayer S4Arrays S4Vectors scales snow snowfall SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Mmusculus.UCSC.mm10.knownGene txdbmaker tzdb UCSC.utils utf8 VariantAnnotation vctrs viridisLite vroom withr XML xml2 XVector yaml zlibbioc

Biscuiteer User Guide

Rendered frombiscuiteer.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-12-06
Started: 2019-10-17

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Convenience Functions for Biscuit	biscuiteer-package biscuiteer _PACKAGE
Summarize a bsseq dataset over defined regions	atRegions
Bin CpG or CpH coverage to simplify and improve CNA "sketching"	binCoverage
bsseq class methods (VCF-centric) added by biscuiteer	biscuiteer-methods BSseq-methods coverage fixed,BSseq-method geno,BSseq,ANY-method header header,BSseq-method info,BSseq-method meta,BSseq-method reference samples,BSseq-method
Biscuit metadata from VCF header	biscuitMetadata getBiscuitMetadata
A simple parallization step	byChromArm
Choose loci or features by extremality	byExtremality
Inspect Biscuit VCF and BED files	checkBiscuitBED
clocks	clocks
Simplify sample names for a bsseq object	condenseSampleNames
Measure methylation status for PRCs or PMDs	CpGindex
ENSR_subset data from hg19 genome	ENSR_subset.hg19
ENSR_subset data from hg38 genome	ENSR_subset.hg38
Compute fraction of a Bernoulli variance	extremality
Helper function: expanded expit	fexpit
Filter loci with zero coverage	filterLoci
Turn 'epigenetic clock' into actual age	fixAge
Replace NAs with another value	fixNAs
Helper function: squeezed logit	flogit
Retrieve 'epigenetic clock' models	getClock
Helper function for compartment inference	getLogitFracMeth getMvals
GRCh37.chromArm	GRCh37.chromArm
GRCh38.chromArm	GRCh38.chromArm
Dump GRanges to segmented data data.frame	grToSeg
H9state23unmeth.hg19	H9state23unmeth.hg19
H9state23unmeth.hg38	H9state23unmeth.hg38
hg19.chromArm	hg19.chromArm
hg38.chromArm	hg38.chromArm
HMM_CpG_islands.hg19	HMM_CpG_islands.hg19
HMM_CpG_islands.hg38	HMM_CpG_islands.hg38
Make an in-memory bsseq object from a biscuit BED	makeBSseq
Read biscuit output into bsseq object	loadBiscuit readBiscuit
Read in and decode the RLE representation of the epibed format out of biscuit epiread	readEpibed
(e)RRBS settings for dmrseq	RRBSeq
Import a segmentation file into GRanges object	segToGr
seqinfo.hg19	seqinfo.hg19
seqinfo.hg38	seqinfo.hg38
seqinfo.mm10	seqinfo.mm10
Simplify bsseq sample names	simplifySampleNames
Summarize methylation over provided regions	summarizeBsSeqOver
Read from tabix-indexed bed file to list objects	tabixRetrieve
Combine bsseq objects together without losing information	unionize
Guess ages using Horvath-style 'clock' models	WGBSage
Wrapper for WGBS settings for dmrseq	WGBSeq