FourCSeq: Package analyse 4C sequencing data

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("FourCSeq")
AuthorFelix A. Klein, EMBL Heidelberg
Bioconductor views Preprocessing Sequencing Software
Date of publicationNone
MaintainerFelix A. Klein <felix.klein@embl.de>
LicenseGPL (>= 3)
Version1.8.0

View on Bioconductor

Functions

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

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

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