Table 2. Table showing run times and memory usage for CAMPP applied to datasets of different sizes.

As the weighted gene co-expression network analysis (WGCNA) and estimation of optimal number of clusters for k-means are by far the slowest and most memory consuming processes, we have provided estimates with and without these two analyses. The [.] denotes that a given analysis was not performed on a dataset.

	Type of Data	Biological Type	Number of Samples	Number of Variables	WGCNA Variables	K-means	Interaction Networks	Run Time in Minutes	Memory Usage in GB
Dataset 1	Mass Spectrometry	N-glycans	80	165	All	Yes	.	0,3	0,6
Dataset 2	Array	mRNA	80	15000	.	.	.	0,8	0,8
Dataset 2	Array	mRNA	80	15000	Differentially Expressed	Yes	.	3,3	1,4
Dataset 2	Array	mRNA	80	15000	All	.	.	12	7,8
Dataset 2	Array	mRNA	80	15000	All	Yes	.	15,5	7,8
Dataset 3	Array + Array	microRNA + mRNA	80	15754	.	.	Yes	4	1,6
Dataset 3	Array + Array	microRNA + mRNA	80	15754	Differentially Expressed	Yes	Yes	5,6	1,6
Dataset 3	Array + Array	microRNA + mRNA	80	15754	All	.	Yes	16	7,8
Dataset 4	Array	mRNA	80	29274	.	.	.	1,2	0,9
Dataset 4	Array	mRNA	80	29274	Differentially Expressed	Yes	.	3,8	1,9
Dataset 5	Sequencing	mRNA	416	55150	.	.	.	3	1,5
Dataset 5	Sequencing	mRNA	416	55150	Differentially Expressed	.	.	3,5	1,4
Dataset 5	Sequencing	mRNA	416	55150	Differentially Expressed	Yes	.	12,8	2,3