DChIPRep: DChIPRep - Analysis of chromatin modification ChIP-Seq data with replication

The DChIPRep package implements a methodology to assess differences between chromatin modification profiles in replicated ChIP-Seq studies as described in Chabbert et. al - http://www.dx.doi.org/10.15252/msb.20145776. A detailed description of the method is given in the software paper at https://doi.org/10.7717/peerj.1981

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("DChIPRep")
AuthorBernd Klaus [aut, cre], Christophe Chabbert [aut], Sebastian Gibb [ctb]
Bioconductor views ChIPSeq Sequencing
Date of publicationNone
MaintainerBernd Klaus <bernd.klaus@embl.de>
LicenseMIT + file LICENCE
Version1.6.0

View on Bioconductor

Functions

chip_galonska Man page
DChIPRep Man page
DChIPRep-package Man page
DChIPRepResults Man page
DChIPRepResults-class Man page
DESeq2Data Man page
DESeq2Data<- Man page
DESeq2Data<-,DChIPRepResults,DESeqDataSet-method Man page
DESeq2Data,DChIPRepResults-method Man page
exampleChipData Man page
exampleInputData Man page
exampleSampleTable Man page
FDRresults Man page
FDRresults<- Man page
FDRresults<-,DChIPRepResults,list-method Man page
FDRresults,DChIPRepResults-method Man page
getMATfromDataFrame Man page
importData Man page
importDataFromMatrices Man page
importData_soGGi Man page
input_galonska Man page
plotProfiles Man page
plotProfiles,DChIPRepResults-method Man page
plotSignificance Man page
plotSignificance,DChIPRepResults-method Man page
resultsDChIPRep Man page
resultsDChIPRep<- Man page
resultsDChIPRep<-,DChIPRepResults,list-method Man page
resultsDChIPRep,DChIPRepResults-method Man page
runTesting Man page
runTesting,DChIPRepResults-method Man page
sample_table_galonska Man page
show Man page
show,DChIPRepResults-method Man page
summarizeCountsPerPosition Man page
testData Man page
TSS_galonska Man page

Files

DESCRIPTION
LICENCE
NAMESPACE
NEWS
R
R/AllClasses.R R/AllGenerics.R R/DChipRep.R R/dataImport.R R/dataImportsoGGi.R R/documentData.R R/methods.R R/plottingFunctions.R R/runTesting.R
build
build/vignette.rds
data
data/TSS_galonska.rda
data/chip_galonska.rda
data/exampleChipData.rda
data/exampleInputData.rda
data/exampleSampleTable.rda
data/input_galonska.rda
data/sample_table_galonska.rda
data/testData.rda
exec
exec/DChIPRep.py
inst
inst/CITATION
inst/REFERENCES.bib
inst/doc
inst/doc/DChIPRepVignette.R
inst/doc/DChIPRepVignette.Rmd
inst/doc/DChIPRepVignette.html
inst/extdata
inst/extdata/BY_conf_K4me3_1__ORF_count.txt
inst/extdata/BY_conf_K4me3_2__ORF_count.txt
inst/extdata/BY_conf_K4me3_3__ORF_count.txt
inst/extdata/BY_conf_WCE_1__ORF_count.txt
inst/extdata/BY_conf_WCE_2__ORF_count.txt
inst/extdata/BY_conf_WCE_3__ORF_count.txt
inst/extdata/SET2_conf_K4me3_1__ORF_count.txt
inst/extdata/SET2_conf_K4me3_2__ORF_count.txt
inst/extdata/SET2_conf_K4me3_3__ORF_count.txt
inst/extdata/SET2_conf_WCE_1__ORF_count.txt
inst/extdata/SET2_conf_WCE_2__ORF_count.txt
inst/extdata/SET2_conf_WCE_3__ORF_count.txt
inst/extdata/subsampled_0001_pc_SRR2144628_WCE_bowtie2_mapped-only_XS-filt_no-dups.bam
inst/extdata/subsampled_0001_pc_SRR2144628_WCE_bowtie2_mapped-only_XS-filt_no-dups.bam.bai
man
man/DChIPRep.Rd man/DChIPRepResults.Rd man/DESeq2Data.Rd man/FDRresults.Rd man/TSS_galonska.Rd man/chip_galonska.Rd man/exampleChipData.Rd man/exampleInputData.Rd man/exampleSampleTable.Rd man/getMATfromDataFrame.Rd man/importData.Rd man/importDataFromMatrices.Rd man/importData_soGGi.Rd man/input_galonska.Rd man/plotProfiles.Rd man/plotSignificance.Rd man/resultsDChIPRep.Rd man/runTesting.Rd man/sample_table_galonska.Rd man/show.Rd man/summarizeCountsPerPosition.Rd man/testData.Rd
tests
tests/testthat
tests/testthat.R tests/testthat/test_Testing.R tests/testthat/test_dataImport.R tests/testthat/test_dataImport_soGGi.R tests/testthat/test_dataInput.R tests/testthat/test_plottingFunctions.R tests/testthat/test_testConstructor.R
vignettes
vignettes/DChIPRepVignette.Rmd
vignettes/references.bib

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