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.

AuthorFelix A. Klein, EMBL Heidelberg
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

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

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