Science Score: 36.0%
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
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✓DOI references
Found 2 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
5 of 19 committers (26.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (6.2%) to scientific vocabulary
Keywords
bioinformatics
dna-methylation
microarray
Keywords from Contributors
bioconductor-package
gene
genomics
bioconductor
core-package
u24ca289073
ontology
grna-sequence
proteomics
tumor-mutational-burden
Last synced: 6 months ago
·
JSON representation
Repository
🍪 SEnsible Step-wise Analysis of DNA MEthylation BeadChips
Basic Info
Statistics
- Stars: 78
- Watchers: 6
- Forks: 37
- Open Issues: 118
- Releases: 0
Topics
bioinformatics
dna-methylation
microarray
Created about 8 years ago
· Last pushed about 1 year ago
Metadata Files
Readme
License
README.md
SeSAMe - SEnsible Step-wise Analysis of Methylation data
SeSAMe is an R package for processing Infinium DNA methylation data. SeSAMe currently supports EPIC, HM450 and HM27 platforms and dynamically generated manifest.
To install from Github,
R
BiocManager::install("zwdzwd/sesame")
See the package Home Page on Bioconductor and the Developmental Branch.
It also has a depended data package for annotation and example data.
Bugs
Bug reports are appreciated. Register issues at the SeSAMe issue tracker.
About
Please cite and reference SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions for more details.
Owner
- Name: Wanding Zhou - Bioinformatics
- Login: zwdzwd
- Kind: user
- Location: Philadelphia
- Company: Children's Hospital of Philadelphia
- Repositories: 5
- Profile: https://github.com/zwdzwd
Working on Computational Epigenetics at CHOP and UPenn
GitHub Events
Total
- Issues event: 23
- Watch event: 19
- Issue comment event: 29
- Push event: 3
- Pull request event: 5
- Fork event: 10
Last Year
- Issues event: 23
- Watch event: 19
- Issue comment event: 29
- Push event: 3
- Pull request event: 5
- Fork event: 10
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Wanding Zhou | z****g@g****m | 535 |
| Wanding Zhou | w****u@v****g | 325 |
| Wanding Zhou | z****3@e****u | 67 |
| elaineficarra | 8****a | 23 |
| Ethan Moyer | e****r@g****m | 22 |
| ttriche | t****e@g****m | 19 |
| Wubin Ding | d****n@1****m | 16 |
| Nitesh Turaga | n****a@g****m | 14 |
| Ethan Moyer | 5****r | 11 |
| Vince Carey | s****c@c****u | 7 |
| vobencha | v****a@g****m | 2 |
| Goldberg | g****2@p****u | 2 |
| J Wokaty | j****y@s****u | 2 |
| J Wokaty | j****y | 2 |
| Elaine Ficarra | e****a@E****e | 1 |
| Zhou | z****3@c****u | 1 |
| Zhou | w****u@C****l | 1 |
| LiNk-NY | m****9@g****m | 1 |
| Henrik Bengtsson | hb@a****g | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 96
- Total pull requests: 31
- Average time to close issues: 2 months
- Average time to close pull requests: 16 days
- Total issue authors: 73
- Total pull request authors: 13
- Average comments per issue: 3.33
- Average comments per pull request: 0.35
- Merged pull requests: 18
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 22
- Pull requests: 4
- Average time to close issues: 25 days
- Average time to close pull requests: 19 days
- Issue authors: 19
- Pull request authors: 4
- Average comments per issue: 0.55
- Average comments per pull request: 1.25
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- Pancreas-Pratik (5)
- priyatamapandey (4)
- claus-h-g (4)
- alanlamsiu (4)
- jdreyf (4)
- OluwayioseOA (3)
- ardan33 (3)
- jcm6t (2)
- JBinkowski (2)
- YoannPa (2)
- tiagochst (2)
- WalterPavicic (2)
- Oluwatobiloba98 (2)
- DKaukonen (2)
- altuda (2)
Pull Request Authors
- ethanmoyer (7)
- ttriche (5)
- golddc (4)
- DingWB (4)
- elaineficarra (3)
- njspix (2)
- adamtolnay (2)
- bethan-mallabar-rimmer (2)
- HenrikBengtsson (1)
- vjcitn (1)
- Kabilan108 (1)
- Pancreas-Pratik (1)
- snowpong (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 73,058 total
- Total dependent packages: 4
- Total dependent repositories: 0
- Total versions: 7
- Total maintainers: 1
bioconductor.org: sesame
SEnsible Step-wise Analysis of DNA MEthylation BeadChips
- Homepage: https://github.com/zwdzwd/sesame
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/sesame/inst/doc/sesame.pdf
- License: MIT + file LICENSE
-
Latest release: 1.26.0
published 10 months ago
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 5.6%
Downloads: 16.7%
Maintainers (1)
Last synced:
6 months ago
Dependencies
DESCRIPTION
cran
- R >= 4.2.0 depends
- sesameData * depends
- BiocFileCache * imports
- BiocParallel * imports
- GenomeInfoDb * imports
- GenomicRanges * imports
- IRanges * imports
- MASS * imports
- S4Vectors * imports
- SummarizedExperiment * imports
- dplyr * imports
- ggplot2 * imports
- graphics * imports
- grid * imports
- illuminaio * imports
- methods * imports
- preprocessCore * imports
- readr * imports
- reshape2 * imports
- stats * imports
- stringr * imports
- tibble * imports
- utils * imports
- wheatmap >= 0.2.0 imports
- BiocStyle * suggests
- DNAcopy * suggests
- RPMM * suggests
- e1071 * suggests
- ggrepel * suggests
- grDevices * suggests
- knitr * suggests
- pals * suggests
- randomForest * suggests
- rmarkdown * suggests
- scales * suggests
- testthat * suggests
- tidyr * suggests