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

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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

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