Science Score: 33.0%
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
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○.zenodo.json file
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✓DOI references
Found 1 DOI reference(s) in README -
✓Academic publication links
Links to: biorxiv.org, ncbi.nlm.nih.gov -
✓Committers with academic emails
3 of 8 committers (37.5%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (7.6%) to scientific vocabulary
Repository
MethCP
Basic Info
Statistics
- Stars: 5
- Watchers: 1
- Forks: 2
- Open Issues: 1
- Releases: 0
Metadata Files
README.md
methcp: An R package for Differentially Methylated Region Detection
MethCP is an R package for analyzing whole-genome bisulfite sequencing (WGBS) data. It implements MethCP algorithm introduced in (Gong and Purdom, 2018).
MethCP detects differentially methylated region for WGBS data based on change point detection, which naturally segments the genome and provide region-level differential analysis. It uses as input the results of a per-nucleotide test-statistic, like DSS or methylKit, and uses this input to segment the genome into regions. Then, several meta-analysis strategies are provided to identify which of those regions are DMR.
To install the package:
```R if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("MethCP") ```
Alternatively, to install the current version on Github:
r
library(devtools)
install_github("boyinggong/methcp", dependencies=TRUE,
repos=BiocInstaller::biocinstallRepos())
A tutorial can be found here.
Contact: Boying Gong(boyinggong@berkeley.edu).
Owner
- Name: Boying Gong
- Login: boyinggong
- Kind: user
- Location: Berkeley, CA
- Company: University of California, Berkeley
- Repositories: 6
- Profile: https://github.com/boyinggong
GitHub Events
Total
Last Year
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Boying Gong | b****g@B****l | 17 |
| Boying Gong | b****g@h****m | 7 |
| Boying Gong | b****g@a****u | 4 |
| Boying Gong | b****g@b****u | 4 |
| Boying Gong | b****g@b****t | 2 |
| Nitesh Turaga | n****a@g****m | 2 |
| Boying Gong | b****g@b****t | 1 |
| Boying Gong | b****g@a****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: over 1 year ago
All Time
- Total issues: 1
- Total pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 1
- Total pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- desmodus1984 (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 2,971 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 1
- Total maintainers: 1
bioconductor.org: MethCP
Differential methylation anlsysis for bisulfite sequencing data
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/MethCP/inst/doc/MethCP.pdf
- License: Artistic-2.0
- Status: removed
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Latest release: 1.13.0
published over 2 years ago