Data

Tools

Indexes

Applications

Experiments

Open Source Science

CNVfilteR

R package to remove false positives of CNV calling tools by using SNV calls

https://github.com/jpuntomarcos/cnvfilter

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 5 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 8 committers (12.5%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.3%) to scientific vocabulary

Keywords from Contributors

bioconductor-package genomics gene grna-sequence immune-repertoire ontology sequencing bioconductor bioinformatics proteomics
Last synced: 11 months ago · JSON representation

Repository

R package to remove false positives of CNV calling tools by using SNV calls

Basic Info
  • Host: GitHub
  • Owner: jpuntomarcos
  • Language: R
  • Default Branch: master
  • Size: 1.07 MB
Statistics
  • Stars: 6
  • Watchers: 1
  • Forks: 1
  • Open Issues: 2
  • Releases: 0
Created almost 7 years ago · Last pushed almost 3 years ago
Metadata Files
Readme

README.md

CNVfilteR

R package to remove false positives of CNV calling tools by using SNV calls

Introduction

Many tools for germline copy number variant (CNV) detection from NGS data have been developed. Usually, these tools were designed for different input data like WGS, WES or panel data, and their performance may depend on the CNV size. Available benchmarks show that all these tools obtain false positives, sometimes reaching a very high number of them.

With the aim of reducing the number of false positives, CNVfilteR identifies those germline CNVs that can be discarded. This task is performed by using the germline single nucleotide variant (SNV) calls that are usually obtained in common NGS pipelines. As VCF field interpretation is key when working with these files, CNVfilteR specifically supports VCFs produced by VarScan2, Strelka/Strelka2, freeBayes, HaplotypeCaller, UnifiedGenotyper and Torrent Variant Caller. Additionally, results can be plotted using the functions provided by the R/Bioconductor packages karyoploteR and CopyNumberPlots.

How to use it

Documentation (vignette and user manual) are available at the CNVfilteR Bioconductor site, allow with instructions to install it.

Citation

CNVfilteR was developed by José Marcos Moreno-Cabrera and Bernat Gel. For citations, please refer to the Bioinformatics paper:

José Marcos Moreno-Cabrera, Jesús del Valle, Elisabeth Castellanos, Lidia Feliubadaló, Marta Pineda, Eduard Serra, Gabriel Capellá, Conxi Lázaro, Bernat Gel, CNVfilteR: an R/Bioconductor package to identify false positives produced by germline NGS CNV detection tools, Bioinformatics, 2021;, btab356, https://doi.org/10.1093/bioinformatics/btab356

Owner

  • Name: José Marcos Moreno-Cabrera
  • Login: jpuntomarcos
  • Kind: user
  • Location: L'Hospitalet de Llobregat, Barcelona
  • Company: IDIBELL

Bioinformatician and software engineer at IDIBELL.

GitHub Events

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

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 177
  • Total Committers: 8
  • Avg Commits per committer: 22.125
  • Development Distribution Score (DDS): 0.446
Past Year
  • Commits: 15
  • Committers: 3
  • Avg Commits per committer: 5.0
  • Development Distribution Score (DDS): 0.267
Top Committers
Name Email Commits
jpuntomarcos j****s@g****m 98
jpuntomarcos a****y 33
Jose Marcos Moreno j****o@w****l 20
Nitesh Turaga n****a@g****m 12
Bernat Gel b****l@g****m 8
J Wokaty j****y@s****u 2
José Marcos Moreno-Cabrera j****c@i****t 2
J Wokaty j****y 2
Committer Domains (Top 20 + Academic)
idibell.cat: 1 sph.cuny.edu: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 11
  • Total pull requests: 3
  • Average time to close issues: 29 days
  • Average time to close pull requests: about 1 hour
  • Total issue authors: 8
  • Total pull request authors: 1
  • Average comments per issue: 3.82
  • Average comments per pull request: 0.33
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: about 2 hours
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • PengZhangJHU (2)
  • AndreaG5 (2)
  • sunjh22 (2)
  • georgiiprovisor (1)
  • HengqiLiu (1)
  • CNHAustin (1)
  • goldpm1 (1)
  • dpacohen (1)
Pull Request Authors
  • bernatgel (3)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 9,653 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 6
  • Total maintainers: 1
bioconductor.org: CNVfilteR

Identifies false positives of CNV calling tools by using SNV calls

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 9,653 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 25.6%
Downloads: 76.8%
Maintainers (1)
jpuntomarcos@gmail.com
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.3 depends
  • Biostrings * imports
  • CopyNumberPlots * imports
  • GenomeInfoDb * imports
  • GenomicRanges * imports
  • IRanges * imports
  • Rsamtools * imports
  • SummarizedExperiment * imports
  • VariantAnnotation * imports
  • assertthat * imports
  • graphics * imports
  • karyoploteR * imports
  • methods * imports
  • pracma * imports
  • regioneR * imports
  • utils * imports
  • BSgenome.Hsapiens.UCSC.hg19 * suggests
  • BSgenome.Hsapiens.UCSC.hg19.masked * suggests
  • BiocStyle * suggests
  • knitr * suggests
  • rmarkdown * suggests