R: Robust Tests for Differential Dispersion and Differential Expression in RNA-Sequencing Data

# Robust Tests for Differential Dispersion and Differential Expression in RNA-Sequencing Data

## Documentation for package ‘DiPhiSeq’ version 0.2.0

- DESCRIPTION file.

## Help Pages

diphiseq | Main function. For most users, this function is all what they need for the analysis.
example_data | Numeric count matrix of example data.
outprop | Give a rough estimate of the proportion of outliers in the data based on the results of DiPhiSeq.
robnb | Calculates the estimate and standard error of beta and phi. It takes as input counts from one group of samples for a single gene. This function is the core underlining function of the whole package. A significant part of the code is edited based on William H. Aeberhard's glmrob.nb R function; we appreciate them very much for sharing their code online. This function also implement Algorithm 1 of our submitted paper about DiPhiSeq. This function is called by robtest. Most users don't need to call this function directly.
robtest | Calls the robnb function to estimate the coefficients, and then construct the statistical tests for DD and DE. It works for a single gene. y1 and y2 are count vectors for a single gene. diphiseq calls this function to do the calculation for each gene. Normal users often don't need to use this function directly.