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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("r3Cseq")
AuthorSupat Thongjuea, MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, UK <supat.thongjuea@ndcls.ox.ac.uk>
Bioconductor views Preprocessing Sequencing
Date of publicationNone
MaintainerSupat Thongjuea <supat.thongjuea@ndcls.ox.ac.uk>
LicenseGPL-3
Version1.22.0
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

Functions

calculateBatchRPM Man page
calculateBatchRPM,r3CseqInBatch-method Man page
calculateRPM Man page
calculateRPM,r3Cseq-method Man page
contrCoverage Man page
contrCoverage,r3Cseq-method Man page
contrInteractionRegions Man page
contrInteractionRegions,r3CseqCommon-method Man page
contrRawData Man page
contrRawData<- Man page
contrRawData<-,r3Cseq-method Man page
contrRawData,r3Cseq-method Man page
contrReadCount Man page
contrReadCount,r3CseqCommon-method Man page
contrRPM Man page
contrRPM,r3CseqCommon-method Man page
enzymeDb Man page
expCoverage Man page
expCoverage,r3Cseq-method Man page
expInteractionRegions Man page
expInteractionRegions,r3CseqCommon-method Man page
export3Cseq2bedGraph Man page
export3Cseq2bedGraph,r3Cseq-method Man page
export3CseqRawReads2bedGraph Man page
export3CseqRawReads2bedGraph,r3Cseq-method Man page
exportBatchInteractions2text Man page
exportBatchInteractions2text,r3CseqInBatch-method Man page
exportInteractions2text Man page
exportInteractions2text,r3Cseq-method Man page
expRawData Man page
expRawData<- Man page
expRawData<-,r3Cseq-method Man page
expRawData,r3Cseq-method Man page
expReadCount Man page
expReadCount,r3CseqCommon-method Man page
expRPM Man page
expRPM,r3CseqCommon-method Man page
generate3CseqReport Man page
generate3CseqReport,r3CseqInBatch-method Man page
generate3CseqReport,r3Cseq-method Man page
getBatchInteractions Man page
getBatchInteractions,r3CseqInBatch-method Man page
getBatchRawReads Man page
getBatchRawReads,r3CseqInBatch-method Man page
getBatchReadCountPerRestrictionFragment Man page
getBatchReadCountPerRestrictionFragment,r3CseqInBatch-method Man page
getBatchReadCountPerWindow Man page
getBatchReadCountPerWindow,r3CseqInBatch-method Man page
getContrInteractionsInRefseq Man page
getContrInteractionsInRefseq,r3Cseq-method Man page
getCoverage Man page
getCoverage,r3Cseq-method Man page
getExpInteractionsInRefseq Man page
getExpInteractionsInRefseq,r3Cseq-method Man page
getInteractions Man page
getInteractions,r3Cseq-method Man page
getRawReads Man page
getRawReads,r3Cseq-method Man page
getReadCountPerRestrictionFragment Man page
getReadCountPerRestrictionFragment,r3Cseq-method Man page
getReadCountPerWindow Man page
getReadCountPerWindow,r3Cseq-method Man page
getViewpoint Man page
getViewpoint,r3Cseq-method Man page
hg18refGene Man page
hg19refGene Man page
mm10refGene Man page
mm9refGene Man page
Myb_prom_FB Man page
Myb_prom_FL Man page
plot3Cecdf Man page
plot3Cecdf,r3Cseq-method Man page
plotDomainogramNearViewpoint Man page
plotDomainogramNearViewpoint,r3Cseq-method Man page
plotInteractionsNearViewpoint Man page
plotInteractionsNearViewpoint,r3Cseq-method Man page
plotInteractionsPerChromosome Man page
plotInteractionsPerChromosome,r3Cseq-method Man page
plotOverviewInteractions Man page
plotOverviewInteractions,r3Cseq-method Man page
r3Cseq Man page
r3Cseq-class Man page
r3CseqCommon Man page
r3CseqCommon-class Man page
r3CseqInBatch Man page
r3CseqInBatch-class Man page
rn5refGene Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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All documentation is copyright its authors; we didn't write any of that.