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https://github.com/bioconductor-source/rnbeads

https://github.com/bioconductor-source/rnbeads

Science Score: 13.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
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    DOI references
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    Academic publication links
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (3.2%) to scientific vocabulary
Last synced: 9 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: bioconductor-source
  • Language: R
  • Default Branch: devel
  • Size: 4.85 MB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created almost 2 years ago · Last pushed almost 2 years ago
Metadata Files
Readme

README 

RnBeads is an R package for comprehensive analysis of DNA methylation data
obtained with any experimental protocol that provides single-CpG resolution,
including Infinium 450K microarray and bisulfite sequencing protocols, but also
MeDIP-seq and MBD-seq once the data have been preprocessed with
DNA methylation inference software. RnBeads implements an analysis workflow
that is significantly more comprehensive than those of existing tools. 
It documents its results in a highly annotated and readable hypertext report,
and it scales to the large sample sizes that are becoming the norm for
DNA methylation analysis in human cohorts.

Owner

  • Name: (WIP DEV) Bioconductor Packages
  • Login: bioconductor-source
  • Kind: organization
  • Email: maintainer@bioconductor.org

Source code for packages accepted into Bioconductor

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Dependencies

DESCRIPTION cran
  • BiocGenerics * depends
  • GenomicRanges * depends
  • MASS * depends
  • R >= 3.0.0 depends
  • S4Vectors >= 0.9.25 depends
  • cluster * depends
  • ff * depends
  • fields * depends
  • ggplot2 >= 0.9.2 depends
  • gplots * depends
  • grid * depends
  • gridExtra * depends
  • illuminaio * depends
  • limma * depends
  • matrixStats * depends
  • methods * depends
  • methylumi * depends
  • plyr * depends
  • IRanges * imports
  • Category * suggests
  • GOstats * suggests
  • Gviz * suggests
  • IlluminaHumanMethylation450kanno.ilmn12.hg19 * suggests
  • IlluminaHumanMethylation450kmanifest * suggests
  • MethylSeekR * suggests
  • RPMM * suggests
  • RUnit * suggests
  • RnBeads.hg19 * suggests
  • RnBeads.hg38 * suggests
  • RnBeads.mm9 * suggests
  • XML * suggests
  • annotate * suggests
  • argparse * suggests
  • biomaRt * suggests
  • doParallel * suggests
  • foreach * suggests
  • ggbio * suggests
  • glmnet * suggests
  • hexbin * suggests
  • impute * suggests
  • isva * suggests
  • mclust * suggests
  • mgcv * suggests
  • minfi * suggests
  • missMethyl * suggests
  • nlme * suggests
  • org.Hs.eg.db * suggests
  • org.Mm.eg.db * suggests
  • org.Rn.eg.db * suggests
  • plotrix * suggests
  • quadprog * suggests
  • qvalue * suggests
  • rtracklayer * suggests
  • scales * suggests
  • sesame * suggests
  • shiny * suggests
  • shinyjs * suggests
  • sva * suggests
  • wateRmelon * suggests
  • wordcloud * suggests