FourCSeq: Package analyse 4C sequencing data
Version 1.10.0

FourCSeq is an R package dedicated to the analysis of (multiplexed) 4C sequencing data. The package provides a pipeline to detect specific interactions between DNA elements and identify differential interactions between conditions. The statistical analysis in R starts with individual bam files for each sample as inputs. To obtain these files, the package contains a python script (extdata/python/demultiplex.py) to demultiplex libraries and trim off primer sequences. With a standard alignment software the required bam files can be then be generated.

AuthorFelix A. Klein, EMBL Heidelberg
Bioconductor views Preprocessing Sequencing Software
Date of publicationNone
MaintainerFelix A. Klein <felix.klein@embl.de>
LicenseGPL (>= 3)
Version1.10.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("FourCSeq")

Popular man pages

addPeaks: Add peaks based on z-scores and adjusted p-values
countFragmentOverlapsSecondCutter: Count fragment overlaps when sequencing was performed from...
findViewpointFragments: Find the fragments to which the viewpoint primers map.
getAllResults: FourCSeq analysis results
getZScores: Calculate z-scores using the residuals of the general trend...
normalizeRPM: Normalize count data to rpm
plotFits: Plot fit results.
See all...

All man pages Function index File listing

Man pages

addFragments: Add the restriction fragment information
addPeaks: Add peaks based on z-scores and adjusted p-values
addViewpointFrags: Add the information of the viewpoint fragments
combineFragEnds: Combine the counts of both fragment ends.
countFragmentOverlaps: Count fragment overlaps
countFragmentOverlapsSecondCutter: Count fragment overlaps when sequencing was performed from...
distFitMonotone: Fit the distance dependency
distFitMonotoneSymmetric: Fit the distance dependency
fc: FourC object with counts
fcf: FourC object with z-scores
findViewpointFragments: Find the fragments to which the viewpoint primers map.
FourC: FourC-class
getAllResults: FourCSeq analysis results
getDifferences: Detect differences
getDistAroundVp: getDistAroundVp
getNormalizationFactors: Get normalization factors for each fragment
getReferenceSeq: Function to read reference sequences
getZScores: Calculate z-scores using the residuals of the general trend...
normalizeRPM: Normalize count data to rpm
plotDifferences: Plot differences
plotFits: Plot fit results.
plotNormalizationFactors: Plot the estimated normalization factors.
plotScatter: plotScatter
plotZScores: Plot z-score results.
smoothCounts: Smooth the counts of neighboring fragments
smoothHitPerCent: Smooth the hits of neighboring fragments
writeTrackFiles: Write track files of an selected 'assay'

Functions

FourC Man page Source code
FourC-class Man page
addFragments Man page Source code
addPeaks Man page Source code
addViewpointFrags Man page Source code
combineFragEnds Man page Source code
countFragmentOverlaps Man page Source code
countFragmentOverlapsSecondCutter Man page Source code
distFitMonotone Man page Source code
distFitMonotoneSymmetric Man page Source code
fc Man page
fcf Man page
findViewpointFragments Man page Source code
getAllResults Man page Source code
getDifferences Man page Source code
getDistAroundVp Man page Source code
getFragments Source code
getNormalizationFactors Man page Source code
getReferenceSeq Man page Source code
getSites Source code
getVST Source code
getZScores Man page Source code
normalizeRPM Man page Source code
plotDifferences Man page Source code
plotFits Man page Source code
plotNormalizationFactors Man page Source code
plotScatter Man page Source code
plotSmoothScatter Source code
plotVp Source code
plotZScores Man page Source code
saveGR Source code
smoothCounts Man page Source code
smoothHitPerCent Man page Source code
updateObject,FourC-method Man page
writeTrackFiles Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/classes.R
R/functions.R
R/plotResults.R
R/reference_fragments.R
build
build/vignette.rds
data
data/datalist
data/fc.rda
data/fcf.rda
inst
inst/CITATION
inst/doc
inst/doc/FourCSeq.R
inst/doc/FourCSeq.Rnw
inst/doc/FourCSeq.pdf
inst/extdata
inst/extdata/bam
inst/extdata/bam/CRM_ap_ApME680_MESO_6-8h_1_testdata.bam
inst/extdata/bam/CRM_ap_ApME680_MESO_6-8h_1_testdata.bam.bai
inst/extdata/bam/CRM_ap_ApME680_MESO_6-8h_2_testdata.bam
inst/extdata/bam/CRM_ap_ApME680_MESO_6-8h_2_testdata.bam.bai
inst/extdata/bam/CRM_ap_ApME680_WE_3-4h_1_testdata.bam
inst/extdata/bam/CRM_ap_ApME680_WE_3-4h_1_testdata.bam.bai
inst/extdata/bam/CRM_ap_ApME680_WE_3-4h_2_testdata.bam
inst/extdata/bam/CRM_ap_ApME680_WE_3-4h_2_testdata.bam.bai
inst/extdata/bam/CRM_ap_ApME680_WE_6-8h_1_testdata.bam
inst/extdata/bam/CRM_ap_ApME680_WE_6-8h_1_testdata.bam.bai
inst/extdata/bam/CRM_ap_ApME680_WE_6-8h_2_testdata.bam
inst/extdata/bam/CRM_ap_ApME680_WE_6-8h_2_testdata.bam.bai
inst/extdata/dm3_chr2L_1-6900.fa
inst/extdata/primer.fa
inst/extdata/python
inst/extdata/python/demultiplex.py
man
man/FourC.Rd
man/addFragments.Rd
man/addPeaks.Rd
man/addViewpointFrags.Rd
man/combineFragEnds.Rd
man/countFragmentOverlaps.Rd
man/countFragmentOverlapsSecondCutter.Rd
man/distFitMonotone.Rd
man/distFitMonotoneSymmetric.Rd
man/fc.Rd
man/fcf.Rd
man/findViewpointFragments.Rd
man/getAllResults.Rd
man/getDifferences.Rd
man/getDistAroundVp.Rd
man/getNormalizationFactors.Rd
man/getReferenceSeq.Rd
man/getZScores.Rd
man/normalizeRPM.Rd
man/plotDifferences.Rd
man/plotFits.Rd
man/plotNormalizationFactors.Rd
man/plotScatter.Rd
man/plotZScores.Rd
man/smoothCounts.Rd
man/smoothHitPerCent.Rd
man/writeTrackFiles.Rd
vignettes
vignettes/FourCSeq.Rnw
vignettes/literature.bib
vignettes/readmapping.pdf
FourCSeq documentation built on May 20, 2017, 9:30 p.m.

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