HIMA is an R package for estimating and testing high-dimensional mediation effects in omic studies. HIMA can perform high-dimensional mediation analysis on a wide range of omic data types as potential mediators, including epigenetics, transcriptomics, proteomics, metabolomics, and microbiomics. HIMA can also handle survival data mediation analysis and perform quantile mediation analysis.
| Package: | HIMA |
| Type: | Package |
| Version: | 2.3.0 |
| Date: | 2025-01-27 |
| License: | GPL-3 |
Details
# If package "qvalue" is not found during installation, please first install "qvalue" package # through Bioconductor: https://www.bioconductor.org/packages/release/bioc/html/qvalue.html
References
1. Zhang H, Zheng Y, Zhang Z, Gao T, Joyce B, Yoon G, Zhang W, Schwartz J, Just A, Colicino E, Vokonas P, Zhao L, Lv J, Baccarelli A, Hou L, Liu L. Estimating and Testing High-dimensional Mediation Effects in Epigenetic Studies. Bioinformatics. 2016. DOI: 10.1093/bioinformatics/btw351. PMID: 27357171; PMCID: PMC5048064
2. Zhang H, Zheng Y, Hou L, Zheng C, Liu L. Mediation Analysis for Survival Data with High-Dimensional Mediators. Bioinformatics. 2021. DOI: 10.1093/bioinformatics/btab564. PMID: 34343267; PMCID: PMC8570823
3. Zhang H, Chen J, Feng Y, Wang C, Li H, Liu L. Mediation Effect Selection in High-dimensional and Compositional Microbiome data. Stat Med. 2021. DOI: 10.1002/sim.8808. PMID: 33205470; PMCID: PMC7855955
4. Zhang H, Chen J, Li Z, Liu L. Testing for Mediation Effect with Application to Human Microbiome Data. Stat Biosci. 2021. DOI: 10.1007/s12561-019-09253-3. PMID: 34093887; PMCID: PMC8177450
5. Perera C, Zhang H, Zheng Y, Hou L, Qu A, Zheng C, Xie K, Liu L. HIMA2: High-dimensional Mediation Analysis and Its Application in Epigenome-wide DNA Methylation Data. BMC Bioinformatics. 2022. DOI: 10.1186/s12859-022-04748-1. PMID: 35879655; PMCID: PMC9310002
6. Zhang H, Hong X, Zheng Y, Hou L, Zheng C, Wang X, Liu L. High-Dimensional Quantile Mediation Analysis with Application to a Birth Cohort Study of Mother–Newborn Pairs. Bioinformatics. 2024. DOI: 10.1093/bioinformatics/btae055. PMID: 38290773; PMCID: PMC10873903
7. Bai X, Zheng Y, Hou L, Zheng C, Liu L, Zhang H. An Efficient Testing Procedure for High-dimensional Mediators with FDR Control. Statistics in Biosciences. 2024. DOI: 10.1007/s12561-024-09447-4.
Author
Yinan Zheng y-zheng@northwestern.edu, Haixiang Zhang haixiang.zhang@tju.edu.cn, Lei liu (Contact) lei.liu@wustl.edu
Maintainer: Yinan Zheng y-zheng@northwestern.edu