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REMP

Github repository for REMP

https://github.com/yinanzheng/remp

Science Score: 33.0%

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 6 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: ncbi.nlm.nih.gov
  • ✓
    Committers with academic emails
    2 of 11 committers (18.2%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.4%) to scientific vocabulary

Keywords from Contributors

bioconductor-package bioconductor bioinformatics u24ca289073 proteomics core-package gene cell-free-dna copy-number loh
Last synced: 10 months ago · JSON representation

Repository

Github repository for REMP

Basic Info
  • Host: GitHub
  • Owner: YinanZheng
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 303 KB
Statistics
  • Stars: 2
  • Watchers: 1
  • Forks: 2
  • Open Issues: 0
  • Releases: 0
Created almost 9 years ago · Last pushed about 4 years ago
Metadata Files
Readme

README.md

REMP: Repetitive Element Methylation Prediction

REMP provides machine learning-based tools to predict DNA methylation of locus-specific repetitive elements (RE) by learning surrounding genetic and epigenetic information. These tools provide genomewide and single-base resolution of DNA methylation prediction on RE that are difficult to measure directly using array-based or sequencing-based platforms, which enables epigenome-wide association study (EWAS) and differentially methylated region (DMR) analysis on RE.

Supporting methylation platforms: + Illumina 450k BeadChip Array + Illumina EPIC BeadChip Array + Illumina methylation sequencing platforms (e.g., TruSeq Methyl Capture EPIC)

Installation

REMP is available in Bioconductor repository ```r

try http:// if https:// URLs are not supported

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

To get the latest version of REMP, please make sure you are using the latest Bioconductor

Install REMP

BiocManager::install("REMP") ```

Citation:

Zheng Y, Joyce BT, Liu L, Zhang Z, Kibbe WA, Zhang W, Hou L. Prediction of genome-wide DNA methylation in repetitive elements. Nucleic Acids Research. 2017;45(15):8697-711. PubMed PMID: 28911103; PMCID: PMC5587781. http://dx.doi.org/10.1093/nar/gkx587.

Contact package maintainer:

Yinan Zheng

Email: y-zheng@northwestern.edu

Owner

  • Name: Yinan Zheng
  • Login: YinanZheng
  • Kind: user
  • Location: Chicago

Assistant Professor at Northwestern University Feinberg School of Medicine

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 65
  • Total Committers: 11
  • Avg Commits per committer: 5.909
  • Development Distribution Score (DDS): 0.492
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Yinan Zheng y****g@n****u 33
Nitesh Turaga n****a@g****m 14
Jane z****1@c****u 5
Herve Pages h****s@f****g 3
Hervé Pagès h****s@f****g 2
vobencha v****n@r****g 2
vobencha v****a@g****m 2
Kayla-Morrell k****l@r****g 1
Martin Morgan m****n@f****g 1
LiNk-NY m****9@g****m 1
Hervé Pagès h****b@g****m 1
Committer Domains (Top 20 + Academic)
roswellpark.org: 2 fhcrc.org: 2 fredhutch.org: 1 case.edu: 1 northwestern.edu: 1

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 3
  • Total pull requests: 0
  • Average time to close issues: 3 months
  • Average time to close pull requests: N/A
  • Total issue authors: 3
  • Total pull request authors: 0
  • Average comments per issue: 2.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • 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
  • krissaMAC (1)
  • yeswzc (1)
  • BastienNguyen (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 12,833 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 3
  • Total maintainers: 1
bioconductor.org: REMP

Repetitive Element Methylation Prediction

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 12,833 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 18.5%
Downloads: 55.5%
Maintainers (1)
y-zheng@northwestern.edu
Last synced: over 1 year ago

Dependencies

DESCRIPTION cran
  • R >= 3.6 depends
  • SummarizedExperiment >= 1.1.6 depends
  • minfi >= 1.22.0 depends
  • AnnotationHub * imports
  • BSgenome * imports
  • BiocGenerics * imports
  • BiocParallel * imports
  • Biostrings * imports
  • GenomeInfoDb * imports
  • GenomicRanges * imports
  • IRanges * imports
  • S4Vectors * imports
  • caret * imports
  • doParallel * imports
  • foreach * imports
  • graphics * imports
  • impute * imports
  • iterators * imports
  • kernlab * imports
  • methods * imports
  • org.Hs.eg.db * imports
  • parallel * imports
  • ranger * imports
  • readr * imports
  • rtracklayer * imports
  • settings * imports
  • stats * imports
  • utils * imports
  • BSgenome.Hsapiens.UCSC.hg19 * suggests
  • BSgenome.Hsapiens.UCSC.hg38 * suggests
  • IlluminaHumanMethylation450kanno.ilmn12.hg19 * suggests
  • IlluminaHumanMethylationEPICanno.ilm10b2.hg19 * suggests
  • knitr * suggests
  • minfiDataEPIC * suggests
  • rmarkdown * suggests