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