BinQuasi |
Analyzing Replicated ChIP Sequencing Data Using Quasi-Likelihood |
BQ |
Call peaks in replicated ChIP-seq data using BinQuasi |
call.peaks |
Call peaks from a list of window-level p-values |
coef.glm |
Extract model coefficients |
count.table |
Create a matrix of ChIP-seq count data |
NBDev |
Fit a negative binomial GLM for a given design matrix |
PoisDev |
Compute Poisson deviances for a given design matrix |
QL.fit |
Fit quasi-likelihood models to replicated ChIP-seq data partitioned into a count matrix |
QL.results |
Obtain p- and q-values using results from 'QL.fit' |