FourCSeq: Package analyse 4C sequencing data

Share:

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.

Author
Felix A. Klein, EMBL Heidelberg
Date of publication
None
Maintainer
Felix A. Klein <felix.klein@embl.de>
License
GPL (>= 3)
Version
1.8.0

View on Bioconductor

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'

Files in this package

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