r3Cseq: Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)

This package is an implementation of data analysis for the long-range interactions from 3C-seq assay.

AuthorSupat Thongjuea, MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, UK <supat.thongjuea@ndcls.ox.ac.uk>
Date of publicationNone
MaintainerSupat Thongjuea <supat.thongjuea@ndcls.ox.ac.uk>
LicenseGPL-3
Version1.20.0
http://r3cseq.genereg.net

View on Bioconductor

Man pages

calculateBatchRPM: calculate read per million (RPM) for replicates analysis

calculateRPM: calculate read per million (RPM)

contrCoverage: This method has been removed.

contrInteractionRegions: get interaction regions from the control

contrRawData: Accessors for the 'contrRawData' slot of a r3Cseq object.

contrReadCount: get read count per region for the control

contrRPM: get read per million (RPM) for the control

enzymeDb: Rebase The Restriction Enzyme Database

expCoverage: This method has been removed.

expInteractionRegions: get interaction regions from the experiment

export3Cseq2bedGraph: export interaction regions to the 'bedGraph' format

export3CseqRawReads2bedGraph: export the interaction signal from the raw reads to the...

exportBatchInteractions2text: export identified interaction regions to the tab separated...

exportInteractions2text: export identified interaction regions to the tab separated...

expRawData: Accessors for the 'expRawData' slot of a r3Cseq object.

expReadCount: get read count per region for the experiment

expRPM: get read per million (RPM) for the experiment

generate3CseqReport: generate reports for analysis results from r3Cseq

getBatchInteractions: calculate z-score, assign p-value and q-value for each...

getBatchRawReads: Get aligned reads from the replicates BAM files

getBatchReadCountPerRestrictionFragment: count reads for replicates analysis

getBatchReadCountPerWindow: count reads per window size for replicates analysis

getContrInteractionsInRefseq: identified significant interaction regions for RefSeq genes

getCoverage: This method has been removed.

getExpInteractionsInRefseq: identified significant interaction regions for RefSeq genes

getInteractions: calculate z-score, assign p-value and q-value for each...

getRawReads: Get aligned reads from the BAM file

getReadCountPerRestrictionFragment: count reads per resitrcition fragment

getReadCountPerWindow: count reads per window size

getViewpoint: get the viewpoint of 3C-seq data

hg18refGene: hg18's refGenes

hg19refGene: hg19's refGenes

mm10refGene: mm10's refGenes

mm9refGene: mm9's refGenes

Myb_prom_FB: Myb_prom_FB a data set for the example of r3Cseq analysis

Myb_prom_FL: Myb_prom_FL a data set for the example of r3Cseq analysis

plot3Cecdf: This method has been removed.

plotDomainogramNearViewpoint: Plot domainogram of interaction regions near the viewpoint

plotInteractionsNearViewpoint: Plot identified interaction regions near the viewpoint

plotInteractionsPerChromosome: Plot interaction regions per each chromosome of interest

plotOverviewInteractions: Plot overview of identified interaction regions for...

r3Cseq-class: r3Cseq objects

r3CseqCommon-class: r3CseqCommon objects

r3CseqInBatch-class: r3CseqInBatch objects

rn5refGene: rn5's refGenes

Files in this package

r3Cseq/DESCRIPTION
r3Cseq/NAMESPACE
r3Cseq/NEWS
r3Cseq/R
r3Cseq/R/AllClasses.R r3Cseq/R/AllGenerics.R r3Cseq/R/Annotation.R r3Cseq/R/Export.R r3Cseq/R/FunctionInCommon.R r3Cseq/R/FunctionsForBatchAnalysis.R r3Cseq/R/FunctionsForNoReplicationAnalysis.R r3Cseq/R/Report.R r3Cseq/R/RestrictionEnzymeFunctions.R r3Cseq/R/Visualize3Cseq.R
r3Cseq/build
r3Cseq/build/vignette.rds
r3Cseq/data
r3Cseq/data/Myb_prom_FB.rdata
r3Cseq/data/Myb_prom_FL.rdata
r3Cseq/data/datalist
r3Cseq/data/enzymeDb.rda
r3Cseq/data/example.data.rda
r3Cseq/data/hg18refGene.rdata
r3Cseq/data/hg19refGene.rdata
r3Cseq/data/mm10refGene.rdata
r3Cseq/data/mm9refGene.rdata
r3Cseq/data/rn5refGene.rdata
r3Cseq/inst
r3Cseq/inst/doc
r3Cseq/inst/doc/r3Cseq.R
r3Cseq/inst/doc/r3Cseq.Rnw
r3Cseq/inst/doc/r3Cseq.pdf
r3Cseq/man
r3Cseq/man/Myb_prom_FB.Rd r3Cseq/man/Myb_prom_FL.Rd r3Cseq/man/calculateBatchRPM.Rd r3Cseq/man/calculateRPM.Rd r3Cseq/man/contrCoverage.Rd r3Cseq/man/contrInteractionRegions.Rd r3Cseq/man/contrRPM.Rd r3Cseq/man/contrRawData.Rd r3Cseq/man/contrReadCount.Rd r3Cseq/man/enzymeDb.Rd r3Cseq/man/expCoverage.Rd r3Cseq/man/expInteractionRegions.Rd r3Cseq/man/expRPM.Rd r3Cseq/man/expRawData.Rd r3Cseq/man/expReadCount.Rd r3Cseq/man/export3Cseq2bedGraph.Rd r3Cseq/man/export3CseqRawReads2bedGraph.Rd r3Cseq/man/exportBatchInteractions2text.Rd r3Cseq/man/exportInteractions2text.Rd r3Cseq/man/generate3CseqReport.Rd r3Cseq/man/getBatchInteractions.Rd r3Cseq/man/getBatchRawReads.Rd r3Cseq/man/getBatchReadCountPerRestrictionFragment.Rd r3Cseq/man/getBatchReadCountPerWindow.Rd r3Cseq/man/getContrInteractionsInRefseq.Rd r3Cseq/man/getCoverage.Rd r3Cseq/man/getExpInteractionsInRefseq.Rd r3Cseq/man/getInteractions.Rd r3Cseq/man/getRawReads.Rd r3Cseq/man/getReadCountPerRestrictionFragment.Rd r3Cseq/man/getReadCountPerWindow.Rd r3Cseq/man/getViewpoint.Rd r3Cseq/man/hg18refGene.Rd r3Cseq/man/hg19refGene.Rd r3Cseq/man/mm10refGene.Rd r3Cseq/man/mm9refGene.Rd r3Cseq/man/plot3Cecdf.Rd r3Cseq/man/plotDomainogramNearViewpoint.Rd r3Cseq/man/plotInteractionsNearViewpoint.Rd r3Cseq/man/plotInteractionsPerChromosome.Rd r3Cseq/man/plotOverviewInteractions.Rd r3Cseq/man/r3Cseq-class.Rd r3Cseq/man/r3CseqCommon-class.Rd r3Cseq/man/r3CseqInBatch-class.Rd r3Cseq/man/rn5refGene.Rd
r3Cseq/vignettes
r3Cseq/vignettes/images
r3Cseq/vignettes/images/3CseqProcedures.png
r3Cseq/vignettes/images/r3CseqFlowChart.png
r3Cseq/vignettes/r3Cseq.Rnw
r3Cseq/vignettes/r3Cseq.bib

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