Introduction

This page contains the datasets used in

Pereira, M. B., Wallroth, M., Jonsson, V., Kristiansson, E., Comparison of normalization methods for the analysis of metagenomic gene abundance data, submitted to Microbiome, 2017.


Gene count data used in the study

Human gut I (from Qin et al., 2012)
Human gut II (from Yatsunenko et al., 2012)
Marine (from Sunagawa et al., 2015)


References

Qin, J., Li, Y., Cai, Z., Li, S., Zhu, J., Zhang, F., Liang, S., Zhang, W., Guan, Y., Shen, D., Peng, Y., Zhang, D., Jie, Z., Wu, W., Qin, Y., Xue, W., Li, J., Han, L., Lu, D., Wu, P., Dai, Y., Sun, X., Li, Z., Tang, A., Zhong, S., Li, X., Chen, W., Xu, R., Wang, M., Feng, Q., Gong, M., Yu,J., Zhang, Y., Zhang, M., Hansen, T., Sanchez, G., Raes, J., Falony, G., Okuda, S., Almeida, M., LeChatelier, E., Renault, P., Pons, N., Batto, J. M., Zhang, Z., Chen, H., Yang, R., Zheng, W., Yang, H., Wang, J., Ehrlich, S. D., Nielsen, R., Pedersen, O., and Kristiansen, K. (2012). A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature, 490(7418):55-60.

Sunagawa, S., Coelho, L. P., Chaffron, S., Kultima, J. R., Labadie, K., Salazar, G., Djahanschiri, B., Zeller, G., Mende, D. R., Alberti, A., Cornejo-Castillo, F. M., Costea, P. I., Cruaud, C., D'Ovidio, F., Engelen, S., Ferrera, I., Gasol, J. M., Guidi, L., Hildebrand, F., Kokoszka, F., Lepoivre, C., Lima-Mendez, G., Poulain, J., Poulos, B. T., Royo-Llonch, M., Sarmento, H., Vieira-Silva, S., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Bowler, C., de Vargas, C., Gorsky, G., Grimsley, N., Hingamp, P., Iudicone, D., Jaillon, O., Not, F., Ogata, H., Pesant, S., Speich, S., Stemmann, L., Sullivan, M. B., Weissenbach, J., Wincker, P., Karsenti, E., Raes, J., Acinas, S. G., Bork, P., Boss, E., Bowler, C., Follows, M., Karp-Boss, L., Krzic, U., Reynaud, E. G., Sardet, C., Sieracki, M., and Velayoudon, D. (2015). Structure and function of the global ocean microbiome. Science, 348(6237):1261359.

Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R. N., Anokhin, A. P., Heath, A. C., Warner, B., Reeder, J., Kuczynski, J., Caporaso, J. G., Lozupone, C. A., Lauber, C., Clemente, J. C., Knights, D., Knight, R., and Gordon, J. I. (2012). Human gut microbiome viewed across age and geography. Nature, 486(7402):222-227.