Data

Tools

Indexes

Applications

Experiments

Open Source Science

dupRadar

Duplication rate quality control for RNA-Seq datasets.

https://github.com/ssayols/dupradar

Science Score: 49.0%

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
    Found .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 12 committers (8.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.0%) to scientific vocabulary

Keywords from Contributors

bioconductor-package gene genomics proteomics bioc bioconductor pathway-analysis metagenomics cell-free-dna mirror
Last synced: 7 months ago · JSON representation

Repository

Duplication rate quality control for RNA-Seq datasets.

Basic Info
  • Host: GitHub
  • Owner: ssayols
  • License: gpl-3.0
  • Language: R
  • Default Branch: master
  • Size: 15.1 MB
Statistics
  • Stars: 2
  • Watchers: 1
  • Forks: 2
  • Open Issues: 0
  • Releases: 0
Created over 7 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog License

README.md

dupRadar

Assessment of duplication rates in RNA-Seq datasets.

Introduction to dupRadar

PCR clonal artefacts originating from NGS library preparation can affect both genomic as well as RNA-Seq applications when protocols are pushed to their limits. In RNA-Seq however the artifactual reads are not easy to tell apart from normal read duplication due to natural over-sequencing of highly expressed genes. Especially when working with little input material or single cells assessing the fraction of duplicate reads is an important quality control step for NGS data sets. Up to now there are only tools to calculate the global duplication rates that do not take into account the effect of gene expression levels which leaves them of limited use for RNA-Seq data.

Installation

To install this package, start R and enter:

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

BiocManager::install("dupRadar") ```

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

r browseVignettes("dupRadar")

or access the pkgdown documentation.

Dependencies

Imports (mandatory for core functionality)

  • Rsubread: Mapping, quantification and variant analysis of sequencing data.

Citation

Sayols S, Scherzinger D, Klein H (2016). "dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data." BMC Bioinformatics, 17, 428. doi: 10.1186/s12859-016-1276-2.

Owner

  • Name: ssayols
  • Login: ssayols
  • Kind: user

GitHub Events

Total
  • Watch event: 1
  • Issue comment event: 1
  • Push event: 8
  • Pull request event: 1
Last Year
  • Watch event: 1
  • Issue comment event: 1
  • Push event: 8
  • Pull request event: 1

Committers

Last synced: almost 2 years ago

All Time
  • Total Commits: 57
  • Total Committers: 12
  • Avg Commits per committer: 4.75
  • Development Distribution Score (DDS): 0.649
Past Year
  • Commits: 4
  • Committers: 1
  • Avg Commits per committer: 4.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
ssayols s****g@g****m 20
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
James Hester j****r@f****g 2
vobencha v****n@r****g 2
vobencha v****a@g****m 2
zxBIB Sayols_Puig,Sergi (RES) EXTERNAL s****t@b****m 1
J Wokaty j****y 1
ssayols s****s 1
Committer Domains (Top 20 + Academic)
fredhutch.org: 2 fhcrc.org: 2 boehringer-ingelheim.com: 1 roswellpark.org: 1 sph.cuny.edu: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 3
  • Total pull requests: 2
  • Average time to close issues: 2 days
  • Average time to close pull requests: less than a minute
  • Total issue authors: 3
  • Total pull request authors: 1
  • Average comments per issue: 1.67
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • 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
  • Rohit-Satyam (1)
  • tiagochst (1)
  • matdoering (1)
Pull Request Authors
  • ssayols (2)
  • adamrtalbot (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 57,603 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 2
bioconductor.org: dupRadar

Assessment of duplication rates in RNA-Seq datasets

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 57,603 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 5.5%
Downloads: 16.5%
Maintainers (2)
sergisayolspuig@gmail.com holger.klein@gmail.com
Last synced: 7 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.2.0 depends
  • KernSmooth * imports
  • Rsubread >= 1.14.1 imports
  • AnnotationHub * suggests
  • BiocStyle * suggests
  • knitr * suggests
  • rmarkdown * suggests
.github/workflows/pkgdown.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite