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

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

Author
Supat Thongjuea, MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, UK <supat.thongjuea@ndcls.ox.ac.uk>
Date of publication
None
Maintainer
Supat Thongjuea <supat.thongjuea@ndcls.ox.ac.uk>
License
GPL-3
Version
1.20.0
URLs

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