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

AuthorBernd Klaus [aut, cre], Christophe Chabbert [aut], Sebastian Gibb [ctb]
Date of publicationNone
MaintainerBernd Klaus <bernd.klaus@embl.de>
LicenseMIT + file LICENCE
Version1.4.0

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

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.