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methylCC

R/BioC package to estimate the cell composition of whole blood in DNA methylation samples in microarray or sequencing platforms

https://github.com/stephaniehicks/methylcc

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 5 committers (20.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (5.8%) to scientific vocabulary

Keywords from Contributors

bioconductor-package gene immune-repertoire grna-sequence proteomics genomics sequencing ontology data-access next-generation-sequencing
Last synced: 10 months ago · JSON representation

Repository

R/BioC package to estimate the cell composition of whole blood in DNA methylation samples in microarray or sequencing platforms

Basic Info
  • Host: GitHub
  • Owner: stephaniehicks
  • Language: R
  • Default Branch: master
  • Size: 8.86 MB
Statistics
  • Stars: 19
  • Watchers: 5
  • Forks: 6
  • Open Issues: 0
  • Releases: 0
Created almost 9 years ago · Last pushed over 3 years ago
Metadata Files
Readme

README.md

methylCC

Citation

Hicks SC, Irizarry RA. (2019). Genome Biology 20, 261. https://doi.org/10.1186/s13059-019-1827-8

Why use methylCC?

This is a package to estimate the cell composition of whole blood in DNA methylation measured on any platform technology (e.g. Illumina 450K microarray, whole genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS)).

For help with the methylCC R-package, there is a vignette available in the /vignettes folder.

Installing methylCC

The R-package methylCC can be installed from Github using the R package devtools:

Use to install the latest version of methylCC from Github: s library(devtools) install_github("stephaniehicks/methylCC")

It can also be installed using Bioconductor:

```s

install BiocManager from CRAN (if not already installed)

if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager")

install methylCC package

BiocManager::install("methylCC") ```

After installation, the package can be loaded into R. s library(methylCC)

Bug reports

Report bugs as issues on the GitHub repository

Authors

Owner

  • Name: Stephanie Hicks
  • Login: stephaniehicks
  • Kind: user
  • Location: Baltimore, MD
  • Company: Johns Hopkins

Associate Prof at Johns Hopkins Biostatistics

GitHub Events

Total
Last Year

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 25
  • Total Committers: 5
  • Avg Commits per committer: 5.0
  • Development Distribution Score (DDS): 0.52
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Nitesh Turaga n****a@g****m 12
Stephanie Hicks s****s@g****m 9
J Wokaty j****y@s****u 2
John Lawson j****n 1
Hervé Pagès h****b@g****m 1
Committer Domains (Top 20 + Academic)
sph.cuny.edu: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 9
  • Total pull requests: 1
  • Average time to close issues: over 1 year
  • Average time to close pull requests: about 12 hours
  • Total issue authors: 9
  • Total pull request authors: 1
  • Average comments per issue: 2.44
  • Average comments per pull request: 1.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • ttriche (1)
  • stephaniehicks (1)
  • Niinleslie (1)
  • lc716 (1)
  • ChuanJ (1)
  • ben-laufer (1)
  • liuyiying0628 (1)
  • xxz1482 (1)
  • sunyu1010 (1)
Pull Request Authors
  • j-lawson (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 11,040 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: methylCC

Estimate the cell composition of whole blood in DNA methylation samples

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 11,040 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Stargazers count: 5.3%
Forks count: 8.8%
Average: 17.2%
Downloads: 72.0%
Maintainers (1)
shicks19@jhu.edu
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • FlowSorted.Blood.450k * depends
  • R >= 3.6 depends
  • Biobase * imports
  • GenomicRanges * imports
  • IRanges * imports
  • IlluminaHumanMethylation450kanno.ilmn12.hg19 * imports
  • IlluminaHumanMethylation450kmanifest * imports
  • S4Vectors * imports
  • bsseq * imports
  • bumphunter * imports
  • dplyr * imports
  • genefilter * imports
  • magrittr * imports
  • methods * imports
  • minfi * imports
  • plyranges * imports
  • quadprog * imports
  • stats * imports
  • utils * imports
  • BiocGenerics * suggests
  • BiocStyle * suggests
  • ggplot2 * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat >= 2.1.0 suggests
  • tidyr * suggests