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IBM-BIOCOMPUTING LABORATORY Zhejiang University
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ParallelPCC

Software based on multi-core CPU to calculate Pairwise Person Correlation Coefficient of genes

Futao Zhang , Gulei Jin, Meimei Liang  and Jun Zhu

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ParallelPCC is command-line software to find coexpressed gene pairs.First use Information Entropy to pretreat and cut off some genes. Then calculate the Pairwise Correlation Coefficients.Finally do Z-normalization of the coefficients and output the pair whose z-score >= 3.29 as default if the 3rd argument is neglected. You should input 2 or 3, 4, 5 arguments, the first one is the input file and the second is the output! The 3rd, 4th, 5th are optional. The 3rd is the threshold of z-score for output, default as 3.29. The 4th is the fraction to be cut off, default as 3. That means 1/3 of the raw data are abandoned! The 5th is the output count number. That means the first output count number of interactions to be output, default as 100.

How to run

In Windows, the OMP_NUM_THREADS environment variable should be set manually. Its value is recommended  to be the value of NUMBER_OF_PROCESSORS. In Mac, the OMP_NUM_THREADS is the number of the cores in your CPU as default.

The GPU version will release soon.