HIMA-package: High-Dimensional Mediation Analysis for 'Omic' Data
In YinanZheng/HMA: High-Dimensional Mediation Analysis
HIMA-package R Documentation
High-Dimensional Mediation Analysis for 'Omic' Data
Description
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, and metabolomics using function hima and
microbiome data (function microHIMA). HIMA can also handle survival data (function survHIMA).
Package: HIMA
Type: Package
Version: 2.2.2
Date: 2024-04-17
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
Author(s)
Yinan Zheng y-zheng@northwestern.edu,
Haixiang Zhang haixiang.zhang@tju.edu.cn,
Lifang Hou l-hou@northwestern.edu
Lei liu (Contact) lei.liu@wustl.edu
Maintainer: Yinan Zheng y-zheng@northwestern.edu
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. 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
5. 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
YinanZheng/HMA documentation built on April 23, 2024, 4:55 a.m.
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| HIMA-package | R Documentation |
High-Dimensional Mediation Analysis for 'Omic' Data
Description
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, and metabolomics using function hima and
microbiome data (function microHIMA). HIMA can also handle survival data (function survHIMA).
| Package: | HIMA |
| Type: | Package |
| Version: | 2.2.2 |
| Date: | 2024-04-17 |
| 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
Author(s)
Yinan Zheng y-zheng@northwestern.edu, Haixiang Zhang haixiang.zhang@tju.edu.cn, Lifang Hou l-hou@northwestern.edu Lei liu (Contact) lei.liu@wustl.edu
Maintainer: Yinan Zheng y-zheng@northwestern.edu
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. 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
5. 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
R Package Documentation
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