Science Score: 49.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 7 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
2 of 4 committers (50.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (8.6%) to scientific vocabulary
Repository
High-dimensional Mediation Analysis (HIMA)
Basic Info
Statistics
- Stars: 24
- Watchers: 1
- Forks: 16
- Open Issues: 1
- Releases: 0
Metadata Files
README.md
HIMA: High-dimensional Mediation Analysis
HIMA is an R package for estimating and testing high-dimensional mediation effects in omic studies.
Installation
HIMA is now available in R CRAN repository ```r
Install HIMA
install.packages("HIMA") ```
To install from GitHub ```r
Install HIMA from GitHub
library(devtools) install_github("yinanzheng/HIMA") ```
If package "qvalue" is not found, please first install "qvalue" package through Bioconductor: https://www.bioconductor.org/packages/release/bioc/html/qvalue.html
r
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("qvalue")
Documentation
Explore the tutorial for the HIMA package, which provides detailed usage examples and guidelines, at the following tutorial link:
Citation:
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
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
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
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
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
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
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.
Contact package maintainer:
Yinan Zheng
Email: y-zheng@northwestern.edu
Owner
- Name: Yinan Zheng
- Login: YinanZheng
- Kind: user
- Location: Chicago
- Repositories: 2
- Profile: https://github.com/YinanZheng
Assistant Professor at Northwestern University Feinberg School of Medicine
GitHub Events
Total
- Issues event: 5
- Watch event: 3
- Issue comment event: 6
- Push event: 53
- Pull request event: 7
- Create event: 1
Last Year
- Issues event: 5
- Watch event: 3
- Issue comment event: 6
- Push event: 53
- Pull request event: 7
- Create event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Yinan Zheng | y****g@n****u | 73 |
| Jane | z****1@c****u | 9 |
| Erik-Jan van Kesteren | e****n@g****m | 2 |
| Florian | f****1@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 7
- Total pull requests: 15
- Average time to close issues: 9 months
- Average time to close pull requests: about 20 hours
- Total issue authors: 7
- Total pull request authors: 5
- Average comments per issue: 1.14
- Average comments per pull request: 0.13
- Merged pull requests: 13
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 12
- Average time to close issues: 24 days
- Average time to close pull requests: 1 day
- Issue authors: 2
- Pull request authors: 2
- Average comments per issue: 1.0
- Average comments per pull request: 0.08
- Merged pull requests: 10
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- jlhanson5 (1)
- shiyuzhang0522 (1)
- hhhanying (1)
- b-staley (1)
- FloPittion (1)
- mhmism (1)
- hintchun (1)
Pull Request Authors
- YinanZheng (10)
- Cui-yd (2)
- xiaozhenzhen (1)
- vankesteren (1)
- privefl (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- cran 733 last-month
- Total docker downloads: 21,613
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 12
- Total maintainers: 1
cran.r-project.org: HIMA
High-Dimensional Mediation Analysis
- Homepage: https://github.com/YinanZheng/HIMA/
- Documentation: http://cran.r-project.org/web/packages/HIMA/HIMA.pdf
- License: GPL-3
-
Latest release: 2.3.2
published 10 months ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.4.0 depends
- glmnet * depends
- ncvreg * depends
- HDMT * imports
- MASS * imports
- doParallel * imports
- foreach * imports
- hommel * imports
- iterators * imports
- parallel * imports
- stats * imports
- survival * imports
- utils * imports