Package: bsseq 1.43.1
Kasper Daniel Hansen
bsseq: Analyze, manage and store whole-genome methylation data
A collection of tools for analyzing and visualizing whole-genome methylation data from sequencing. This includes whole-genome bisulfite sequencing and Oxford nanopore data.
Authors:
bsseq_1.43.1.tar.gz
bsseq_1.43.1.zip(r-4.5)bsseq_1.43.1.zip(r-4.4)bsseq_1.43.1.zip(r-4.3)
bsseq_1.43.1.tgz(r-4.4-arm64)bsseq_1.43.0.tgz(r-4.4-x86_64)bsseq_1.43.1.tgz(r-4.3-arm64)bsseq_1.43.0.tgz(r-4.3-x86_64)
bsseq_1.43.1.tar.gz(r-4.5-noble)bsseq_1.43.1.tar.gz(r-4.4-noble)
bsseq_1.43.1.tgz(r-4.4-emscripten)bsseq_1.43.1.tgz(r-4.3-emscripten)
bsseq.pdf |bsseq.html✨
bsseq/json (API)
NEWS
| # Install 'bsseq' in R: |
| install.packages('bsseq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/kasperdanielhansen/bsseq/issues
- BS.chr22 - Whole-genome bisulfite sequencing for chromosome 22 from Lister et al.
On BioConductor:bsseq-1.43.0(bioc 3.21)bsseq-1.42.0(bioc 3.20)
Last updated 6 days agofrom:1cce9a0102. Checks:OK: 1 NOTE: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 17 2024 |
| R-4.5-win-x86_64 | NOTE | Dec 17 2024 |
| R-4.5-linux-x86_64 | NOTE | Dec 17 2024 |
| R-4.4-win-x86_64 | NOTE | Dec 17 2024 |
| R-4.4-mac-aarch64 | NOTE | Dec 17 2024 |
| R-4.4-mac-x86_64 | NOTE | Nov 29 2024 |
| R-4.3-win-x86_64 | NOTE | Dec 17 2024 |
| R-4.3-mac-aarch64 | NOTE | Dec 17 2024 |
| R-4.3-mac-x86_64 | NOTE | Nov 29 2024 |
Exports:assayNamesassaysbinomialGoodnessOfFitBSmoothBSmooth.tstatBSseqBSseqStatBSseqTstatchrSelectBSseqcollapseBSseqcombinecombineListdata.frame2GRangesdmrFinderendend<-findLocifindOverlapsfisherTestsgetBSseqgetCoveragegetMethgetStatsgrangeshasBeenSmoothedncolnroworderBSseqoverlapsAnypDatapData<-plotManyRegionsplotRegionpoissonGoodnessOfFitread.bismarkread.modbam2bedread.modkitsampleNamessampleNames<-seqlengthsseqlengths<-seqlevelsseqlevels<-seqnamesseqnames<-showstartstart<-strandstrand<-strandCollapsesubsetByOverlapsupdateObjectwidthwidth<-
Dependencies:abindaskpassassortheadbeachmatBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomeclicodetoolscolorspacecpp11crayoncurldata.tableDelayedArrayDelayedMatrixStatsfarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgluegtoolsHDF5ArrayhttrIRangesjsonlitelabelinglambda.rlatticelifecyclelimmalocfitMatrixMatrixGenericsmatrixStatsmimemunsellopensslpermuteR.methodsS3R.ooR.utilsR6RColorBrewerRcppRCurlrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsscalessnowSparseArraysparseMatrixStatsstatmodSummarizedExperimentsysUCSC.utilsviridisLiteXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Whole-genome bisulfite sequencing for chromosome 22 from Lister et al. | BS.chr22 |
| BSmooth, smoothing bisulfite sequence data | BSmooth |
| Compute t-statistics based on smoothed whole-genome bisulfite sequencing data. | BSmooth.tstat |
| The constructor function for BSseq objects. | BSseq |
| Class BSseq | assayNames,BSseq-method assays,BSseq-method BSseq-class chrSelectBSseq collapseBSseq combine,BSseq,BSseq-method combineList getBSseq hasBeenSmoothed length,BSseq-method orderBSseq pData,BSseq-method pData<-,BSseq,data.frame-method pData<-,BSseq,DataFrame-method sampleNames,BSseq-method sampleNames<-,BSseq,ANY-method show,BSseq-method strandCollapse updateObject,BSseq-method [,BSseq-method |
| Class BSseqStat | BSseqStat BSseqStat-class show,BSseqStat-method updateObject,BSseqStat-method [,BSseqStat,ANY,ANY,ANY-method [,BSseqStat-method |
| Class BSseqTstat | BSseqTstat BSseqTstat-class show,BSseqTstat-method updateObject,BSseqTstat-method [,BSseqTstat,ANY,ANY,ANY-method [,BSseqTstat-method |
| Converts a data frame to a GRanges. | data.frame2GRanges |
| Finds differentially methylated regions for whole genome bisulfite sequencing data. | dmrFinder |
| Find methylation loci in a genome | findLoci |
| Compute Fisher-tests for a BSseq object | fisherTests |
| Classes FWIRanges and FWGRanges | dimnames,arrayRealizationSink-method end,FWGRanges-method end,FWIRanges-method end<-,FWIRanges-method findOverlaps,FWGRanges,FWGRanges-method FWGRanges-class FWIRanges-class names,FWIRanges-method names<-,FWIRanges-method seqnames,FWGRanges-method start,FWGRanges-method start,FWIRanges-method start<-,FWIRanges-method strand,FWGRanges-method width,FWGRanges-method width,FWIRanges-method width<-,FWIRanges-method |
| Obtain coverage for BSseq objects. | getCoverage |
| Obtain methylation estimates for BSseq objects. | getMeth |
| Obtain statistics from a BSseqTstat object | getStats |
| Binomial and poisson goodness of fit statistics for BSSeq objects | binomialGoodnessOfFit chisqGoodnessOfFit plot.chisqGoodnessOfFit poissonGoodnessOfFit print.chisqGoodnessOfFit |
| Class hasGRanges | class:hasGRanges end,hasGRanges-method end<-,hasGRanges-method findOverlaps,GenomicRanges,hasGRanges-method findOverlaps,hasGRanges,GenomicRanges-method findOverlaps,hasGRanges,hasGRanges-method granges,hasGRanges-method hasGRanges hasGRanges-class length,hasGRanges-method overlapsAny,GenomicRanges,hasGRanges-method overlapsAny,hasGRanges,GenomicRanges-method overlapsAny,hasGRanges,hasGRanges-method seqlengths,hasGRanges-method seqlengths<-,hasGRanges-method seqlevels,hasGRanges-method seqlevels<-,hasGRanges-method seqnames,hasGRanges-method seqnames<-,hasGRanges-method start,hasGRanges-method start<-,hasGRanges-method strand,hasGRanges-method strand<-,hasGRanges,ANY-method strand<-,hasGRanges-method subsetByOverlaps,GenomicRanges,hasGRanges-method subsetByOverlaps,hasGRanges,GenomicRanges-method subsetByOverlaps,hasGRanges,hasGRanges-method width,hasGRanges-method width<-,hasGRanges-method [,hasGRanges,ANY,ANY,ANY-method [,hasGRanges-method |
| Plotting BSmooth methylation estimates | plotManyRegions plotRegion |
| Parsing output from the Bismark alignment suite. | read.bismark |
| Construct BSseq objects from nanopore BED files | read.modbam2bed |
| Construct BSseq objects from nanopore BED files | read.modkit |
