User Guide

##Running a Command Line Tool

To run D³E analysis please run D3ECmd.py:

python D3ECmd.py InputFile OutputFile Label1 Label2 [-h] [-m {0,1}] [-t {0,1,2}] [-z {0,1}] [-n {1,0}] [-s {1,0}] [-v]

Mandatory arguments:

• InputFile : a path to the read-count table
• OutputFile : a path to the output file
• Label1 : a common label for the cells of the first type
• Label2 : a common label for the cells of the second type

Optional arguments

• -m (--mode) : run mode (default = 1)
• -test (--test) : test for distribution comparison
• -z (--removeZeos) : if -z is set to 1, all zero enties in the read-count table will be removed prior to analysis (default = 0)
• -n (--normalise) : if -n is set to 1, a normalisation routine will be performed before analysis (default = 1)
• -v (--verbose) : run in verbose mode (default)

##Input File Format

D3ECmd.py accepts a tab-separated read-count table, where rows correspond to genes, and columns correspond to individual cells. The file should have a header row which has the following tab-separated format:

"GeneID	Label<sub>1</sub>	Label<sub>2</sub>	Label<sub>3</sub>	... "

where L_i are the cell type labels. Differential expression analysis can be performed on two cell types at a time.

Each line should start with a gene ID, followed by a sequence of read-counts. Empty lines are ignored.

##Run Modes

D<sup3 can run in two modes, specified by -m (--mode) option:

• Mode 0 : Methods of moments is used to estimate parameters ( fast but less accurate )
• Mode 1 : Bayesian inference is used to estimate parameters ( slow but more accurate, default )

##Distribution comparison methods

D<sup3 uses one of the following distribution comparison tests, specified by -t (--test) option:

• Mode 0: Cramer-von Mises test
• Mode 1: Kolmogorov-Smirnov test
• Mode 2: Anderson-Darling test