normGAM is an R package for normalizing genome architecture mapping (GAM) data. It implements five normalization methods, including normalized linkage disequilibrium (NLD), vanilla coverage (VC), sequential component normalization (SCN), iterative correction and eigenvector decomposition (ICE), and Knight-Ruiz 2-norm (KR2). The normalization procedure can remove known and unknown systematic biases, the known biases including window detection frequency, fragment length, mappability, and GC content.
normGAM package can be downloaded here.
Tong Liu and Zheng Wang. normGAM: an R package to remove systematic biases in genome architecture mapping data. BMC Genomics, 2019, 20(12):1006.
Tong Liu and Zheng Wang. scHiCNorm: a software package to eliminate systematic biases in single-cell Hi-C data. Bioinformatics, 2018, 34(6):1046-1047.
For any questions or suggestions, please contact:
Dr. Zheng Wang
Department of Computer Science
University of Miami