Package: biscuiteer 1.21.0

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'))

Peer review:

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

Datasets:

On BioConductor:biscuiteer-1.21.0(bioc 3.21)biscuiteer-1.20.0(bioc 3.20)

dataimportmethylseqdnamethylation

6.20 score 5 stars 16 scripts 270 downloads 1 mentions 33 exports 171 dependencies

Last updated 2 months agofrom:7fd1d20618. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 20 2024
R-4.5-winWARNINGNov 20 2024
R-4.5-linuxWARNINGNov 20 2024
R-4.4-winWARNINGNov 20 2024
R-4.4-macWARNINGNov 20 2024
R-4.3-winWARNINGNov 20 2024
R-4.3-macWARNINGNov 20 2024

Exports:atRegionsbinCoveragebiscuitMetadatabyChromArmbyExtremalitycheckBiscuitBEDcondenseSampleNamesextremalityfexpitfilterLocifixAgefixedfixNAsflogitgenogetClockgetLogitFracMethgrToSegheaderinfomakeBSseqmetareadBiscuitreadEpibedRRBSeqsamplessegToGrsimplifySampleNamessummarizeBsSeqOvertabixRetrieveunionizeWGBSageWGBSeq

Dependencies:abindAnnotationDbiAnnotationHubannotatraskpassassortheadbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionbiomaRtBiostringsbiscuiteerDatabitbit64bitopsblobBSgenomebsseqbumphuntercachemCGHbaseCGHcallclicliprcodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdigestdmrseqDNAcopydoRNGdplyrExperimentHubfansifarverfastmapfilelockforeachformatRfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2globalsglueGO.dbgraphgtablegtoolsHDF5ArrayhmsHomo.sapienshttrhttr2imputeIRangesisobanditeratorsjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelifecyclelimmalistenvlocfitmagrittrmarrayMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellMus.musculusnlmeopensslorg.Hs.eg.dborg.Mm.eg.dbOrganismDbioutliersparallellypermutepillarpkgconfigplogrplyrpngprettyunitsprogresspurrrQDNAseqqualVR.methodsS3R.ooR.utilsR6rappdirsRBGLRColorBrewerRcppRCurlreadrregioneRreshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowsnowfallSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsystibbletidyrtidyselectTxDb.Hsapiens.UCSC.hg19.knownGeneTxDb.Mmusculus.UCSC.mm10.knownGenetxdbmakertzdbUCSC.utilsutf8VariantAnnotationvctrsviridisLitevroomwithrXMLxml2XVectoryamlzlibbioc

Biscuiteer User Guide

Rendered frombiscuiteer.Rmdusingknitr::rmarkdownon Nov 20 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Convenience Functions for Biscuitbiscuiteer-package biscuiteer _PACKAGE
Summarize a bsseq dataset over defined regionsatRegions
Bin CpG or CpH coverage to simplify and improve CNA "sketching"binCoverage
bsseq class methods (VCF-centric) added by biscuiteerbiscuiteer-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 headerbiscuitMetadata getBiscuitMetadata
A simple parallization stepbyChromArm
Choose loci or features by extremalitybyExtremality
Inspect Biscuit VCF and BED filescheckBiscuitBED
clocksclocks
Simplify sample names for a bsseq objectcondenseSampleNames
Measure methylation status for PRCs or PMDsCpGindex
ENSR_subset data from hg19 genomeENSR_subset.hg19
ENSR_subset data from hg38 genomeENSR_subset.hg38
Compute fraction of a Bernoulli varianceextremality
Helper function: expanded expitfexpit
Filter loci with zero coveragefilterLoci
Turn 'epigenetic clock' into actual agefixAge
Replace NAs with another valuefixNAs
Helper function: squeezed logitflogit
Retrieve 'epigenetic clock' modelsgetClock
Helper function for compartment inferencegetLogitFracMeth getMvals
GRCh37.chromArmGRCh37.chromArm
GRCh38.chromArmGRCh38.chromArm
Dump GRanges to segmented data data.framegrToSeg
H9state23unmeth.hg19H9state23unmeth.hg19
H9state23unmeth.hg38H9state23unmeth.hg38
hg19.chromArmhg19.chromArm
hg38.chromArmhg38.chromArm
HMM_CpG_islands.hg19HMM_CpG_islands.hg19
HMM_CpG_islands.hg38HMM_CpG_islands.hg38
Make an in-memory bsseq object from a biscuit BEDmakeBSseq
Read biscuit output into bsseq objectloadBiscuit readBiscuit
Read in and decode the RLE representation of the epibed format out of biscuit epireadreadEpibed
(e)RRBS settings for dmrseqRRBSeq
Import a segmentation file into GRanges objectsegToGr
seqinfo.hg19seqinfo.hg19
seqinfo.hg38seqinfo.hg38
seqinfo.mm10seqinfo.mm10
Simplify bsseq sample namessimplifySampleNames
Summarize methylation over provided regionssummarizeBsSeqOver
Read from tabix-indexed bed file to list objectstabixRetrieve
Combine bsseq objects together without losing informationunionize
Guess ages using Horvath-style 'clock' modelsWGBSage
Wrapper for WGBS settings for dmrseqWGBSeq