CCREPE (Compositionality Corrected by Renormalization and Permutation) is a package for analysis of sparse compositional data, such as from metagenomic sequencing. It determines the significance of association between features in a composition, using any similarity measure (e.g. Pearson correlation, Spearman correlation, etc.) The package also provides a novel similarity measure, the N-dimensional checkerboard score (NC-score), particularly appropriate to compositions derived from microbial community sequencing data. This results in p-values and false discovery rate q-values corrected for the effects of compositionality.