Data

Tools

Indexes

Applications

Experiments

Open Source Science

BEclear

Correction of batch effects in DNA methylation data

https://github.com/uds-helms/beclear

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 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    2 of 13 committers (15.4%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.0%) to scientific vocabulary

Keywords

batch-effects bioconductor-package dna-methylation latent-factor-model methylation missing-data missing-values rpackage stochastic-gradient-descent

Keywords from Contributors

genomics gene transcriptomics proteomics mass-spectrometry metabolomics peptides digest cleavage diffusion-maps
Last synced: 6 months ago · JSON representation

Repository

Correction of batch effects in DNA methylation data

Basic Info
Statistics
  • Stars: 5
  • Watchers: 1
  • Forks: 0
  • Open Issues: 10
  • Releases: 0
Topics
batch-effects bioconductor-package dna-methylation latent-factor-model methylation missing-data missing-values rpackage stochastic-gradient-descent
Created over 7 years ago · Last pushed almost 3 years ago
Metadata Files
Readme License

README.md

Travis-CI Build Status Coverage Status

BEclear

Description

This package provides functions to detect and correct for batch effects in DNA methylation data. The core function for the data imputation is based on latent factor models and can also be used to predict missing values in any other matrix containing real numbers.

Installation

```r

Installation from Bioconductor

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

```r

Installation of the development version from GitHub

if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools") devtools::installgithub("uds-helms/BEclear", buildopts = c()) ```

Usage example

For example code you can either read the vignette on Bioconductor. Or you can open it local, after you installed the BEclear package with following command:

r browseVignettes("BEclear")

Planned features

If you have a suggestion you could either open an issue or write an email under the following address: Livia.Rasp at gmail.com

Citation

Akulenko, R., Merl, M., & Helms, V. (2016). BEclear: Batch effect detection and adjustment in DNA methylation data. PLoS ONE, 11(8), 1–17. https://doi.org/10.1371/journal.pone.0159921

Owner

  • Name: Helms Group - Saarland University
  • Login: uds-helms
  • Kind: organization
  • Location: Saarbrücken, Germany

Chair of Computational Biology at the Center for Bioinformatics, Saarland University

GitHub Events

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

Committers

Last synced: about 2 years ago

All Time
  • Total Commits: 224
  • Total Committers: 13
  • Avg Commits per committer: 17.231
  • Development Distribution Score (DDS): 0.237
Past Year
  • Commits: 3
  • Committers: 2
  • Avg Commits per committer: 1.5
  • Development Distribution Score (DDS): 0.333
Top Committers
Name Email Commits
David Rasp d****p@g****m 171
David Rasp D****p@g****m 17
Nitesh Turaga n****a@g****m 14
Dan Tenenbaum d****a@f****g 6
Herve Pages h****s@f****g 4
Hervé Pagès h****s@f****g 2
J Wokaty j****y@s****u 2
vobencha v****n@r****g 2
vobencha v****a@g****m 2
David Rasp d****p@l****l 1
Livia Rasp l****p@g****m 1
Markus Merl b****e@g****m 1
Sonali Arora s****a@f****g 1
Committer Domains (Top 20 + Academic)
fhcrc.org: 3 lacdr.leidenuniv.nl: 1 roswellpark.org: 1 sph.cuny.edu: 1 fredhutch.org: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 27
  • Total pull requests: 1
  • Average time to close issues: about 1 month
  • Average time to close pull requests: less than a minute
  • Total issue authors: 3
  • Total pull request authors: 1
  • Average comments per issue: 0.41
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • 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
View more stats
Top Authors
Issue Authors
  • Livia-Rasp (25)
  • Rut-MDLV (1)
Pull Request Authors
  • Livia-Rasp (1)
Top Labels
Issue Labels
enhancement (11) bug (3) performance issue (2)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 21,642 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: BEclear

Correction of batch effects in DNA methylation data

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 21,642 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 17.7%
Downloads: 53.0%
Maintainers (1)
livia.rasp@gmail.com
Last synced: 6 months ago