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

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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

Author
Bernd Klaus [aut, cre], Christophe Chabbert [aut], Sebastian Gibb [ctb]
Date of publication
None
Maintainer
Bernd Klaus <bernd.klaus@embl.de>
License
MIT + file LICENCE
Version
1.4.0

View on Bioconductor

Man pages

chip_galonska
Another example ChIP data set that can be used with...
DChIPRep
DChIPRep: A package for differential analysis of histone...
DChIPRepResults
DChIPRepResults object and constructor
DESeq2Data
Accessors for the 'DESeq2Data' slot of a 'DChIPRepResults'...
exampleChipData
An example ChIP data.
exampleInputData
An example input data.
exampleSampleTable
An example sample table data.frame
FDRresults
Accessor and setter for the 'FDRresults' slot of a...
getMATfromDataFrame
Helper function to turn a data.frame into a matrix and remove...
importData
Import the data after running the Python script
importDataFromMatrices
Import the data from ChiP and input matrices
importData_soGGi
Import the data from bam files directly
input_galonska
Another example Input data set that can be used with...
plotProfiles
Produce a TSS plot of the two conditions in the data
plotSignificance
Produce a plot that colors the positions identified as...
resultsDChIPRep
Accessors and setter for the 'results' slot of a...
runTesting
Run the tests on a DChIPRepResults object.
sample_table_galonska
Another example sample table based on data from rom Galonska...
show
prints the DESeq2Data slot of the DChIPRepResults object
summarizeCountsPerPosition
Helper function to summarize the counts per position
testData
A test DESeqDataSet
TSS_galonska
TSS around called peak regions from Galonska et. al.

Files in this package

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