Package: segmentSeq 2.41.1

Samuel Granjeaud

segmentSeq: Methods for identifying small RNA loci from high-throughput sequencing data

High-throughput sequencing technologies allow the production of large volumes of short sequences, which can be aligned to the genome to create a set of matches to the genome. By looking for regions of the genome which to which there are high densities of matches, we can infer a segmentation of the genome into regions of biological significance. The methods in this package allow the simultaneous segmentation of data from multiple samples, taking into account replicate data, in order to create a consensus segmentation. This has obvious applications in a number of classes of sequencing experiments, particularly in the discovery of small RNA loci and novel mRNA transcriptome discovery.

Authors:Thomas J. Hardcastle [aut], Samuel Granjeaud [cre]

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

# Install 'segmentSeq' in R:
install.packages('segmentSeq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/samgg/segmentseq/issues

Datasets:
  • hSL - Preprocessed 'lociData' object containing likelihoods of methylation at each locus.

On BioConductor:segmentSeq-2.41.1(bioc 3.21)segmentSeq-2.40.0(bioc 3.20)

multiplecomparisonsequencingalignmentdifferentialexpressionqualitycontroldataimport

6.25 score 42 scripts 263 downloads 5 mentions 22 exports 60 dependencies

Last updated 2 months agofrom:ce8078cfb8. Checks:OK: 5 NOTE: 2. Indexed: yes.

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Doc / VignettesOKNov 30 2024
R-4.5-winNOTENov 30 2024
R-4.5-linuxNOTENov 30 2024
R-4.4-winOKNov 30 2024
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R-4.3-macOKNov 30 2024

Exports:averageProfilesclassifySegfindChunksgetCountsgetOverlapsgivenExpressionheuristicSeglociLikelihoodsmergeMethSegsnormaliseNCplotAverageProfileplotGenomeplotMethplotMethDistributionprocessADreadBAMreadGenericreadMethsselectLocishowsummariseLocithresholdFinder

Dependencies:abindaskpassbaySeqBHBiobaseBiocGenericsBiocParallelBiostringsbitopscodetoolscpp11crayoncurlDelayedArraydeldiredgeRformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangeshttrhwriterinterpIRangesjpegjsonlitelambda.rlatticelatticeExtralimmalocfitMASSMatrixMatrixGenericsmatrixStatsmimeopensslpngpwalignR6RColorBrewerRcppRcppEigenRhtslibRsamtoolsS4ArraysS4VectorsShortReadsnowSparseArraystatmodSummarizedExperimentsysUCSC.utilsXVectorzlibbioc

segmentSeq: methods for identifying small RNA loci from high-throughput sequencing data

Thomas J. Hardcastle

Rendered fromsegmentSeq.Rmdusingknitr::rmarkdownon Nov 30 2024.

Last update: 2024-11-04
Started: 2024-11-04

segmentSeq: methods for detecting methylation loci and differential methylation

Thomas J. Hardcastle

Rendered frommethylationAnalysis.Rmdusingknitr::rmarkdownon Nov 30 2024.

Last update: 2024-11-04
Started: 2024-11-04

Readme and manuals

Help Manual

Help pageTopics
Segmentation of the genome based on multiple samples of high-throughput sequencing data.segmentSeq-package segmentSeq
Class "alignmentClass"alignmentClass alignmentClass-class cbind,alignmentClass-method dim,alignmentClass-method initialize,alignmentClass-method show,alignmentClass-method [,alignmentClass,ANY,ANY,ANY-method [,alignmentClass,ANY,ANY-method [,alignmentClass,ANY-method [,alignmentClass-method
Class "alignmentData"alignmentData alignmentData-class cbind,alignmentData-method dim,alignmentData-method initialize,alignmentData-method show,alignmentData-method [,alignmentData,ANY,ANY,ANY-method [,alignmentData,ANY,ANY-method [,alignmentData,ANY-method [,alignmentData-method
Class "alignmentMeth"alignmentMeth alignmentMeth-class cbind,alignmentMeth-method dim,alignmentMeth-method initialize,alignmentMeth-method show,alignmentMeth-method [,alignmentMeth,ANY,ANY,ANY-method [,alignmentMeth,ANY,ANY-method [,alignmentMeth,ANY-method [,alignmentMeth-method
Computes and plots the average distribution of aligned reads (taken from an alignmentData object) or methylation (taken from an alignmentMeth object) over a set of coordinates (and optionally the surrounding regions).averageProfiles plotAverageProfile
A method for defining a genome segment map by an empirical Bayesian classification methodclassifySeg
Identifies `chunks' of data within a set of aligned reads.findChunks
Gets counts from alignment data from a set of genome segments.getCounts
Identifies overlaps between two sets of genomic coordinatesgetOverlaps
Adjusts posterior likelihoods of differential expression by the likelihood that a locus is expressed.givenExpression
A (fast) heuristic method for creation of a genome segment map.heuristicSeg
Preprocessed 'lociData' object containing likelihoods of methylation at each locus.hSL
Class "lociData"c,lociData-method dim,lociData-method lociData lociData-class show,lociData-method [,lociData,ANY,ANY,ANY-method [,lociData,ANY,ANY-method [,lociData,ANY-method [,lociData-method
Evaluates the posterior likelihoods of each region defined by a segmentation map as a locus.lociLikelihoods
Merges neighbouring methylation loci with the same pattern of expression.mergeMethSegs
Class "methData"dim,methData-method methData methData-class show,methData-method [,methData,ANY,ANY,ANY-method [,methData,ANY,ANY-method [,methData,ANY-method [,methData-method
A function providing adjustment of cytosine methylated/unmethylated counts based on a nonconversion rate.normaliseNC
Plots the alignment of sequence tags on the genome given an `aligmentData' object and (optionally) a set of segments found.plotGenome
Plots a map of cytosine methylation (and optionally, methylation loci).plotMeth
Plots the distribution of methylation on the genome.plotMethDistribution
Processes an `alignmentData' or `alignmentMeth' object into a `segData' or `segMeth' object for segmentation.processAD
Functions for processing files of various formats into an `alignmentData' object.readBAM readGeneric
A function for reading data from the YAMA methylation aligner (or similarly parsed data) from which to identify methylation loci and/or differentially methylated regions.readMeths
Class "segClass"dim,segClass-method initialize,segClass-method segClass segClass-class show,segClass-method [,segClass,ANY,ANY-method [,segClass-method
Class "segData"dim,segData-method initialize,segData-method segData segData-class show,segData-method [,segData,ANY,ANY-method [,segData,ANY-method [,segData-method
Class "segMeth"dim,segMeth-method initialize,segMeth-method segMeth segMeth-class show,segMeth-method [,segMeth,ANY,ANY-method [,segMeth,ANY-method [,segMeth-method
Filters a `lociData' object based on given selection criteria.selectLoci
Example data selected from a set of Illumina sequencing experiments.SL10 SL26 SL32 SL9
Summarise the expected number of loci in a `lociData' object.summariseLoci
Determines threshold for the proportion of methylation at which a methylation locus may be identified.thresholdFinder