GENESIS
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
Science Score: 57.0%
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○CITATION.cff file
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✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 3 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
10 of 22 committers (45.5%) from academic institutions -
✓Institutional organization owner
Organization uw-gac has institutional domain (www.biostat.washington.edu) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (7.6%) to scientific vocabulary
Keywords from Contributors
Repository
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
Basic Info
- Host: GitHub
- Owner: UW-GAC
- Language: R
- Default Branch: devel
- Homepage: https://bioconductor.org/packages/GENESIS
- Size: 3.21 MB
Statistics
- Stars: 38
- Watchers: 8
- Forks: 13
- Open Issues: 16
- Releases: 0
Metadata Files
README.md
GENESIS
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
The GENESIS package provides methodology for estimating, inferring, and accounting for population and pedigree structure in genetic analyses. The current implementation provides functions to perform PC-AiR (Conomos et al., 2015, Gen Epi) and PC-Relate (Conomos et al., 2016, AJHG). PC-AiR performs a Principal Components Analysis on genome-wide SNP data for the detection of population structure in a sample that may contain known or cryptic relatedness. Unlike standard PCA, PC-AiR accounts for relatedness in the sample to provide accurate ancestry inference that is not confounded by family structure. PC-Relate uses ancestry representative principal components to adjust for population structure/ancestry and accurately estimate measures of recent genetic relatedness such as kinship coefficients, IBD sharing probabilities, and inbreeding coefficients. Additionally, functions are provided to perform efficient variance component estimation and mixed model association testing for both quantitative and binary phenotypes.
Bioconductor
Release version
http://www.bioconductor.org/packages/release/bioc/html/GENESIS.html
- Tutorials
- Reference manual
- News
Development version
http://www.bioconductor.org/packages/devel/bioc/html/GENESIS.html
- Tutorials
- Reference manual
- News
Citation
Gogarten, S.M., Sofer, T., Chen, H., Yu, C., Brody, J.A., Thornton, T.A., Rice, K.M., and Conomos, M.P. (2019). Genetic association testing using the GENESIS R/Bioconductor package. Bioinformatics. doi:10.1093/bioinformatics/btz567.
Installation
R
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("GENESIS")
Owner
- Name: GAC
- Login: UW-GAC
- Kind: organization
- Location: Seattle, WA
- Website: https://www.biostat.washington.edu/research/centers/gac
- Repositories: 25
- Profile: https://github.com/UW-GAC
UW Genetic Analysis Center
GitHub Events
Total
- Issues event: 10
- Watch event: 4
- Delete event: 3
- Issue comment event: 11
- Push event: 8
- Pull request event: 7
- Fork event: 1
- Create event: 2
Last Year
- Issues event: 10
- Watch event: 4
- Delete event: 3
- Issue comment event: 11
- Push event: 8
- Pull request event: 7
- Fork event: 1
- Create event: 2
Committers
Last synced: 6 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Stephanie M. Gogarten | s****s@u****u | 362 |
| Matt | m****s@u****u | 148 |
| Adrienne Stilp | a****p@u****u | 135 |
| Matt | m****t@M****l | 31 |
| smgogarten | s****n@v****a | 30 |
| Stephanie Gogarten | s****s@u****u | 17 |
| Nitesh Turaga | n****a@g****m | 14 |
| Matthew Conomos | m****s@D****u | 14 |
| J Wokaty | j****y@s****u | 10 |
| Dan Tenenbaum | d****a@f****g | 8 |
| Herve Pages | h****s@f****g | 5 |
| vobencha | v****a@g****m | 2 |
| Tamar Sofer | t****i | 2 |
| Seth Stadick | s****k@g****m | 2 |
| Hervé Pagès | h****s@f****g | 2 |
| A Wokaty | a****y@s****u | 2 |
| vobencha | v****n@r****g | 2 |
| Sonali Arora | s****a@f****g | 1 |
| mconomos | m****s@m****l | 1 |
| Qiong Yang | q****g@s****u | 1 |
| Qiong Yang | q****g@s****u | 1 |
| Matthew Conomos | m****s@D****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 60
- Total pull requests: 58
- Average time to close issues: 2 months
- Average time to close pull requests: 11 days
- Total issue authors: 43
- Total pull request authors: 9
- Average comments per issue: 2.62
- Average comments per pull request: 1.09
- Merged pull requests: 54
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 8
- Pull requests: 8
- Average time to close issues: 14 days
- Average time to close pull requests: 12 days
- Issue authors: 6
- Pull request authors: 2
- Average comments per issue: 2.13
- Average comments per pull request: 0.0
- Merged pull requests: 8
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- sstadick (4)
- amstilp (4)
- AmandaHWChong (3)
- jonaszierer (3)
- pierreyou (2)
- smgogarten (2)
- yangli-ai (2)
- AAvalos82 (2)
- dleopold (2)
- yu-zhang-oYo (2)
- kaskarn (1)
- BEFH (1)
- candicecjj (1)
- MARCPUCV (1)
- byoo (1)
Pull Request Authors
- smgogarten (25)
- mconomos (13)
- amstilp (10)
- terrytianyuzhang (5)
- qyang10 (2)
- mchughc (1)
- sstadick (1)
- jiwonslee (1)
- tamartsi (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 69,388 total
- Total dependent packages: 1
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: GENESIS
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzing genetic data from samples with population structure and/or relatedness
- Homepage: https://github.com/UW-GAC/GENESIS
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/GENESIS/inst/doc/GENESIS.pdf
- License: GPL-3
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Latest release: 2.38.0
published 10 months ago
Rankings
Maintainers (1)
Dependencies
- Biobase * imports
- BiocGenerics * imports
- BiocParallel * imports
- GWASTools * imports
- GenomicRanges * imports
- IRanges * imports
- Matrix * imports
- S4Vectors * imports
- SNPRelate * imports
- SeqArray * imports
- SeqVarTools * imports
- data.table * imports
- gdsfmt * imports
- grDevices * imports
- graphics * imports
- igraph * imports
- methods * imports
- reshape2 * imports
- stats * imports
- utils * imports
- BiocStyle * suggests
- COMPoissonReg * suggests
- CompQuadForm * suggests
- GGally * suggests
- GWASdata * suggests
- RColorBrewer * suggests
- SPAtest * suggests
- TxDb.Hsapiens.UCSC.hg19.knownGene * suggests
- dplyr * suggests
- ggplot2 * suggests
- knitr * suggests
- poibin * suggests
- rmarkdown * suggests
- survey * suggests
- testthat * suggests