Package: BiSeq 1.45.0

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:Katja Hebestreit, Hans-Ulrich Klein

BiSeq_1.45.0.tar.gz
BiSeq_1.45.0.zip(r-4.5)BiSeq_1.45.0.zip(r-4.4)BiSeq_1.45.0.zip(r-4.3)
BiSeq_1.45.0.tgz(r-4.4-any)BiSeq_1.45.0.tgz(r-4.3-any)
BiSeq_1.45.0.tar.gz(r-4.5-noble)BiSeq_1.45.0.tar.gz(r-4.4-noble)
BiSeq_1.45.0.tgz(r-4.4-emscripten)BiSeq_1.45.0.tgz(r-4.3-emscripten)
BiSeq.pdf |BiSeq.html✨
BiSeq/json (API)

# Install 'BiSeq' in R:

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

Datasets:

DMRs - The output of 'findDMRs'
betaResults - The output of 'betaRegression'
betaResultsNull - The output of 'betaRegression' for resampled data
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-1.45.0(bioc 3.20)BiSeq-1.44.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

37 exports 1.00 score 81 dependencies 33 mentions

Last updated 2 months agofrom:cd005cd510

Exports:annotateGRanges betaRegression binomLikelihoodSmooth BSraw BSrel clusterSites clusterSitesToGR combine compareTwoSamples covBoxplots covStatistics estLocCor filterByCov filterBySharedRegions findDMRs globalTest limitCov logisticRegression makeVariogram methLevel methLevel<-methReads methReads<-plotBindingSites plotMeth plotMethMap plotSmoothMeth predictMeth rawToRel readBismark smoothVariogram summarizeRegions testClusters totalReads totalReads<-trimClusters writeBED

Dependencies:abind annotate AnnotationDbi askpass betareg BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob cachem cli codetools cpp11 crayon curl DBI DelayedArray fastmap flexmix formatR Formula futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges globaltest glue httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle lmtest lokern Matrix MatrixGenerics matrixStats memoise mime modeltools nnet openssl pkgconfig plogr png R6 RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors sandwich sfsmisc snow SparseArray SummarizedExperiment survival sys UCSC.utils vctrs XML xtable XVector yaml zlibbioc zoo

An Introduction to BiSeq

Rendered fromBiSeq.Rnwusingutils::Sweaveon Jun 25 2024.

Last update: 2016-02-22
Started: 2013-11-01

Citation

Development and contributors

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