Introduction | Data import and classes | Quality control | Detection of DMRs within groups of samples | Detection of DMRs between two samples | Testing of predefined genomic regions | Further data processing
Package: BiSeq 1.53.0
Katja Hebestreit
BiSeq: Processing and analyzing bisulfite sequencing data
The BiSeq package provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data. In particular, it implements an algorithm to detect differentially methylated regions (DMRs). The package takes already aligned BS data from one or multiple samples.
Authors:
BiSeq_1.53.0.tar.gz
BiSeq_1.53.0.zip(r-4.7)BiSeq_1.53.0.zip(r-4.6)BiSeq_1.53.0.zip(r-4.5)
BiSeq_1.53.0.tgz(r-4.6-any)BiSeq_1.53.0.tgz(r-4.5-any)
BiSeq_1.53.0.tar.gz(r-4.7-any)BiSeq_1.53.0.tar.gz(r-4.6-any)
BiSeq_1.53.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
BiSeq/json (API)
| # Install 'BiSeq' in R: |
| install.packages('BiSeq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- betaResults - The output of 'betaRegression'
- betaResultsNull - The output of 'betaRegression' for resampled data
- DMRs - The output of 'findDMRs'
- predictedMeth - The output of 'predictMeth'
- promoters - A 'GRanges' of promoters of the human genome
- rrbs - RRBS data of APL patient samples and controls.
- vario - Output of 'makeVariogram'
On BioConductor:BiSeq-1.53.0(bioc 3.24)BiSeq-1.52.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
geneticssequencingmethylseqdnamethylation
Last updated from:773a1eaf9f. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 195 | ||
| linux-devel-x86_64 | NOTE | 425 | ||
| source / vignettes | OK | 308 | ||
| linux-release-x86_64 | NOTE | 382 | ||
| macos-release-arm64 | NOTE | 264 | ||
| macos-oldrel-arm64 | NOTE | 219 | ||
| windows-devel | NOTE | 331 | ||
| windows-release | NOTE | 318 | ||
| windows-oldrel | NOTE | 300 | ||
| wasm-release | OK | 144 |
Exports:annotateGRangesbetaRegressionbinomLikelihoodSmoothBSrawBSrelclusterSitesclusterSitesToGRcombinecompareTwoSamplescovBoxplotscovStatisticsestLocCorfilterByCovfilterBySharedRegionsfindDMRsglobalTestlimitCovlogisticRegressionmakeVariogrammethLevelmethLevel<-methReadsmethReads<-plotBindingSitesplotMethplotMethMapplotSmoothMethpredictMethrawToRelreadBismarksmoothVariogramsummarizeRegionstestClusterstotalReadstotalReads<-trimClusterswriteBED
Dependencies:abindannotateAnnotationDbiaskpassbetaregBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapflexmixformatRFormulafutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesglobaltestgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecyclelmtestlokernMatrixMatrixGenericsmatrixStatsmemoisemimemodeltoolsnnetopensslpkgconfigpngR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssandwichSeqinfosfsmiscsnowSparseArraySummarizedExperimentsurvivalsysvctrsXMLxtableXVectoryamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Annotates a 'GRanges' object by means of a second 'GRanges' object | annotateGRanges annotateGRanges,GRanges,GRanges,character,character-method annotateGRanges,GRanges,GRanges,character,integer-method annotateGRanges,GRanges,GRanges,character,missing-method |
| A function to estimate and test a group factor within a beta regression | betaRegression betaRegression,formula,character,BSrel,missing-method betaRegression,formula,character,BSrel,numeric-method |
| The output of 'betaRegression' | betaResults |
| The output of 'betaRegression' for resampled data | betaResultsNull |
| Calculates local likelihood estimations for binomial random variables | binomLikelihoodSmooth binomLikelihoodSmooth,ANY-method |
| Class to contain raw Bisulfite Sequencing (BiSeq) Data | BSraw BSraw,matrix,matrix,GRanges-method BSraw-class combine,BSraw,BSraw-method methReads methReads,BSraw-method methReads<- methReads<-,BSraw,matrix-method totalReads totalReads,BSraw-method totalReads<- totalReads<-,BSraw,matrix-method |
| Class to contain Bisulfite Sequencing (BiSeq) Data | BSrel BSrel,matrix,GRanges-method BSrel-class combine,BSrel,BSrel-method methLevel methLevel,BSrel-method methLevel<- methLevel<-,BSrel,matrix-method |
| Assigns CpG cluster memberships on CpG sites within 'BSraw' objects | clusterSites clusterSites,BSraw,ANY,numeric,missing,missing,missing-method clusterSites,BSraw,ANY,numeric,missing,numeric,missing-method clusterSites,BSraw,ANY,numeric,numeric,missing,missing-method clusterSites,BSraw,ANY,numeric,numeric,numeric,missing-method clusterSites,BSraw,ANY,numeric,numeric,numeric,numeric-method clusterSites,BSraw,missing,missing,missing,missing,missing-method clusterSites,BSraw,missing,numeric,numeric,numeric,missing-method clusterSites,BSraw,missing,numeric,numeric,numeric,numeric-method |
| A function to obtain a 'GRanges' object of CpG clusters from 'BSraw' and 'BSrel' objects | clusterSitesToGR clusterSitesToGR,BSraw-method clusterSitesToGR,BSrel-method |
| Detects DMRs by comparing two samples | compareTwoSamples compareTwoSamples,BSraw,character,character,numeric,numeric-method compareTwoSamples,BSraw,numeric,numeric,numeric,numeric-method compareTwoSamples,BSrel,character,character,numeric,numeric-method compareTwoSamples,BSrel,numeric,numeric,numeric,numeric-method |
| Creates boxplots of coverages per sample | covBoxplots covBoxplots,BSraw-method |
| Prints a short summary of coverage statistics per sample | covStatistics covStatistics,BSraw-method covStatistics,BSrel-method |
| The output of 'findDMRs' | DMRs |
| Estimates the correlations of the z-scores | estLocCor estLocCor,list-method |
| Filters regions (or single CpGs) of a 'BSraw' object with a minimum coverage | filterByCov filterByCov,BSraw,missing,logical-method filterByCov,BSraw,missing,missing-method filterByCov,BSraw,numeric,logical-method filterByCov,BSraw,numeric,missing-method |
| Reduces a 'BSraw' or 'BSrel' object to regions (or single CpGs) shared by a fraction of samples | filterBySharedRegions filterBySharedRegions,BSraw,ANY,missing,numeric,missing-method filterBySharedRegions,BSraw,ANY,missing,numeric,numeric-method filterBySharedRegions,BSraw,ANY,numeric,missing,missing-method filterBySharedRegions,BSraw,ANY,numeric,missing,numeric-method filterBySharedRegions,BSraw,missing,missing,missing,missing-method filterBySharedRegions,BSraw,missing,missing,missing,numeric-method filterBySharedRegions,BSraw,missing,missing,numeric,missing-method filterBySharedRegions,BSraw,missing,missing,numeric,numeric-method filterBySharedRegions,BSraw,missing,numeric,missing,missing-method filterBySharedRegions,BSraw,missing,numeric,missing,numeric-method filterBySharedRegions,BSrel,ANY,missing,numeric,ANY-method filterBySharedRegions,BSrel,ANY,numeric,missing,ANY-method filterBySharedRegions,BSrel,missing,missing,missing,ANY-method filterBySharedRegions,BSrel,missing,missing,numeric,ANY-method filterBySharedRegions,BSrel,missing,numeric,missing,ANY-method |
| Aggregates CpG sites to DMRs | findDMRs findDMRs,data.frame,missing,numeric,logical-method findDMRs,data.frame,missing,numeric,missing-method findDMRs,data.frame,numeric,numeric,logical-method findDMRs,data.frame,numeric,numeric,missing-method |
| Test whether at least one CpG is differentially methylated in a given genomic region | globalTest globalTest,ANY,BSrel-method |
| Limits the coverage of a 'BSraw' object | limitCov limitCov,BSraw,numeric-method |
| Estimates and tests a group factor | logisticRegression logisticRegression,formula,character,BSrel,missing-method logisticRegression,formula,character,BSrel,numeric-method |
| Variogram estimator. | makeVariogram makeVariogram,data.frame,logical,missing,missing-method makeVariogram,data.frame,logical,missing,numeric-method makeVariogram,data.frame,logical,numeric,missing-method makeVariogram,data.frame,logical,numeric,numeric-method makeVariogram,data.frame,missing,missing,missing-method makeVariogram,data.frame,missing,numeric,numeric-method |
| Plots the mean methylation of given regions | plotBindingSites plotBindingSites,BSraw,GRanges-method plotBindingSites,BSrel,GRanges-method |
| Plots raw and smoothed methylation data for a given region | plotMeth plotMeth,BSraw,BSrel,GRanges-method |
| Plots methylation values of multiple samples in a given region | plotMethMap plotMethMap,BSraw,GRanges,factor,logical-method plotMethMap,BSraw,GRanges,factor,missing-method plotMethMap,BSraw,GRanges,missing,logical-method plotMethMap,BSraw,GRanges,missing,missing-method plotMethMap,BSrel,GRanges,factor,logical-method plotMethMap,BSrel,GRanges,factor,missing-method plotMethMap,BSrel,GRanges,missing,logical-method plotMethMap,BSrel,GRanges,missing,missing-method |
| Plots smoothed methylation values for a bunch of samples and a given region | plotSmoothMeth plotSmoothMeth,BSrel,GRanges,ANY,logical-method plotSmoothMeth,BSrel,GRanges,ANY,missing-method |
| The output of 'predictMeth' | predictedMeth |
| Predicts methylation levels along CpG sites or for a grid of sites in CpG clusters. | predictMeth predictMeth,BSraw,missing,missing,missing-method predictMeth,BSraw,missing,missing,numeric-method predictMeth,BSraw,numeric,missing,missing-method predictMeth,BSraw,numeric,missing,numeric-method predictMeth,BSraw,numeric,numeric,numeric-method |
| A 'GRanges' of promoters of the human genome | promoters |
| Converts a 'BSraw' object to a 'BSrel' object | rawToRel rawToRel,BSraw-method |
| Reads cytosine methylation stati determined by Bismark | readBismark readBismark,character,character-method readBismark,character,data.frame-method readBismark,character,DataFrame-method |
| RRBS data of APL patient samples and controls. | rrbs |
| Smoothes variogram | smoothVariogram smoothVariogram,list,numeric,missing-method smoothVariogram,list,numeric,numeric-method smoothVariogram,matrix,numeric,missing-method smoothVariogram,matrix,numeric,numeric-method |
| Aggregates methylation information of single CpG sites | summarizeRegions summarizeRegions,BSraw,GRanges,logical-method summarizeRegions,BSraw,GRanges,missing-method summarizeRegions,BSrel,GRanges,logical-method summarizeRegions,BSrel,GRanges,missing-method |
| Tests CpG clusters | testClusters testClusters,list,missing-method testClusters,list,numeric-method |
| Trims CpG clusters | trimClusters trimClusters,list,missing-method trimClusters,list,numeric-method |
| Output of 'makeVariogram' | vario |
| Writes 'BSraw' and 'BSrel' data to a bed file suitable for the IGV | writeBED writeBED,BSraw,character,character-method writeBED,BSraw,character,missing-method writeBED,BSraw,missing,character-method writeBED,BSraw,missing,missing-method writeBED,BSrel,character,character-method writeBED,BSrel,character,missing-method writeBED,BSrel,missing,character-method writeBED,BSrel,missing,missing-method |
