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... |
robust_mean | Use a huber type estimator to produce a robust mean |
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. |
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