Learn R Programming

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.

Copy Link

Version

Version

1.18.0

License

GPL-3

Maintainer

Supat Thongjuea

Last Published

February 15th, 2017

Functions in r3Cseq (1.18.0)

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