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r3Cseq (version 1.18.0)
Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)
Description
This package is an implementation of data analysis for the long-range interactions from 3C-seq assay.
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Version
Version
1.18.0
1.16.0
1.14.0
1.12.1
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Version
1.18.0
License
GPL-3
Maintainer
Supat Thongjuea
Last Published
January 1st, 1970
Functions in r3Cseq (1.18.0)
Search functions
contrRPM
get read per million (RPM) for the control
enzymeDb
Rebase The Restriction Enzyme Database
expCoverage
This method has been removed.
getInteractions
calculate z-score, assign p-value and q-value for each interaction region
calculateRPM
calculate read per million (RPM)
plotInteractionsNearViewpoint
Plot identified interaction regions near the viewpoint
hg19refGene
hg19's refGenes
getReadCountPerRestrictionFragment
count reads per resitrcition fragment
plotOverviewInteractions
Plot overview of identified interaction regions for genome-wide
mm9refGene
mm9's refGenes
calculateBatchRPM
calculate read per million (RPM) for replicates analysis
Myb_prom_FB
Myb_prom_FB a data set for the example of r3Cseq analysis
contrInteractionRegions
get interaction regions from the control
getReadCountPerWindow
count reads per window size
plot3Cecdf
This method has been removed.
expRawData
Accessors for the 'expRawData' slot of a r3Cseq object.
r3CseqInBatch-class
r3CseqInBatch objects
rn5refGene
rn5's refGenes
plotInteractionsPerChromosome
Plot interaction regions per each chromosome of interest
hg18refGene
hg18's refGenes
getCoverage
This method has been removed.
r3CseqCommon-class
r3CseqCommon objects
r3Cseq-class
r3Cseq objects
expRPM
get read per million (RPM) for the experiment
Myb_prom_FL
Myb_prom_FL a data set for the example of r3Cseq analysis
exportBatchInteractions2text
export identified interaction regions to the tab separated format for replicates analysis
exportInteractions2text
export identified interaction regions to the tab separated format
getBatchReadCountPerWindow
count reads per window size for replicates analysis
getExpInteractionsInRefseq
identified significant interaction regions for RefSeq genes
contrCoverage
This method has been removed.
contrReadCount
get read count per region for the control
contrRawData
Accessors for the 'contrRawData' slot of a r3Cseq object.
mm10refGene
mm10's refGenes
getBatchRawReads
Get aligned reads from the replicates BAM files
getBatchReadCountPerRestrictionFragment
count reads for replicates analysis
expReadCount
get read count per region for the experiment
export3CseqRawReads2bedGraph
export the interaction signal from the raw reads to the 'bedGraph' format
expInteractionRegions
get interaction regions from the experiment
getRawReads
Get aligned reads from the BAM file
getBatchInteractions
calculate z-score, assign p-value and q-value for each interaction region for replicates data sets
generate3CseqReport
generate reports for analysis results from r3Cseq
export3Cseq2bedGraph
export interaction regions to the 'bedGraph' format
getViewpoint
get the viewpoint of 3C-seq data
getContrInteractionsInRefseq
identified significant interaction regions for RefSeq genes
plotDomainogramNearViewpoint
Plot domainogram of interaction regions near the viewpoint