Man pages for DChIPRep
DChIPRep - Analysis of chromatin modification ChIP-Seq data with replication

chip_galonskaAnother example ChIP data set that can be used with...
DChIPRepDChIPRep: A package for differential analysis of histone...
DChIPRepResultsDChIPRepResults object and constructor
DESeq2DataAccessors for the 'DESeq2Data' slot of a 'DChIPRepResults'...
exampleChipDataAn example ChIP data.
exampleInputDataAn example input data.
exampleSampleTableAn example sample table data.frame
FDRresultsAccessor and setter for the 'FDRresults' slot of a...
getMATfromDataFrameHelper function to turn a data.frame into a matrix and remove...
importDataImport the data after running the Python script
importDataFromMatricesImport the data from ChiP and input matrices
importData_soGGiImport the data from bam files directly
input_galonskaAnother example Input data set that can be used with...
plotProfilesProduce a TSS plot of the two conditions in the data
plotSignificanceProduce a plot that colors the positions identified as...
resultsDChIPRepAccessors and setter for the 'results' slot of a...
robust_meanUse a huber type estimator to produce a robust mean
runTestingRun the tests on a DChIPRepResults object.
sample_table_galonskaAnother example sample table based on data from rom Galonska...
showprints the DESeq2Data slot of the DChIPRepResults object
summarizeCountsPerPositionHelper function to summarize the counts per position
testDataA test DESeqDataSet
TSS_galonskaTSS around called peak regions from Galonska et. al.
DChIPRep documentation built on Nov. 17, 2017, 10:08 a.m.