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CopyNumberPlots

R package to create plots representing copy number data using karyoploteR

https://github.com/bernatgel/copynumberplots

Science Score: 26.0%

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    CITATION.cff file
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    Scientific vocabulary similarity
    Low similarity (11.6%) to scientific vocabulary

Keywords

bioconductor bioconductor-package bioinformatics copy-number-variation genomics genomics-visualization r r-package rstats

Keywords from Contributors

gene grna-sequence sequencing proteomics ontology
Last synced: 6 months ago · JSON representation

Repository

R package to create plots representing copy number data using karyoploteR

Basic Info
  • Host: GitHub
  • Owner: bernatgel
  • Language: R
  • Default Branch: devel
  • Homepage:
  • Size: 2.06 MB
Statistics
  • Stars: 6
  • Watchers: 1
  • Forks: 2
  • Open Issues: 5
  • Releases: 0
Topics
bioconductor bioconductor-package bioinformatics copy-number-variation genomics genomics-visualization r r-package rstats
Created over 7 years ago · Last pushed over 2 years ago
Metadata Files
Readme Changelog

README.md

Project Status: Active – The project has reached a stable, usable state and is being actively developed.

CopyNumberPlots: create copy-number plots using karyoploteR

Introduction

Data visualisation is a powerful tool used for data analysis and exploration in many fields. Genomics data analysis is one of these fields where good visualisation tools can be of great help. The aim of CopyNumberPlots is to offer the user an easy way to create copy-number related plots using the infrastructure provided by the R/Bioconductor package karyoploteR

In addition to a set of specialized plotting functions for copy-number analysis data and results (plotBAF, plotCopyNumberCalls, ...), CopyNumberPlots contains a number of data loading functions to help parsing and loading the results of widely used copy-number calling software such as DNAcopy, DECoN or CNVkit.

Finally, since CopyNumberPlots extends the functionality of karyoploteR, it is possible to combine the plotting functions of both packages to get the perfect figure for your data.

Installation

CopyNumberPlots is a Bioconductor package and to install it we have to use BiocManager

{r getPackage, eval=FALSE} if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("CopyNumberPlots")

More information

You can find more information on CopyNumberPlots in its Bioconductor page and specially in the CopyNumberPlots vignette.

You can find more information on how to use karyoploteR in the karyoploteR tutorial.

Owner

  • Name: Bernat Gel
  • Login: bernatgel
  • Kind: user
  • Location: Barcelona, Spain
  • Company: Germans Trias Research Institute (IGTP)

Bioinformatician at IGTP. Interested in cancer genomics, data analysis and visualization. Working on NF1, Hereditary Cancer and genetic diagnostics.

GitHub Events

Total
Last Year

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 280
  • Total Committers: 4
  • Avg Commits per committer: 70.0
  • Development Distribution Score (DDS): 0.329
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Bernat Gel b****l@g****m 188
Unknown m****o@g****m 74
Nitesh Turaga n****a@g****m 14
J Wokaty j****y 4

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 7
  • Total pull requests: 15
  • Average time to close issues: 13 days
  • Average time to close pull requests: about 1 month
  • Total issue authors: 6
  • Total pull request authors: 1
  • Average comments per issue: 2.29
  • Average comments per pull request: 0.2
  • Merged pull requests: 15
  • 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
  • lbeltrame (2)
  • DarioS (1)
  • moldach (1)
  • lima1 (1)
  • bernatgel (1)
  • ChristianRohde (1)
Pull Request Authors
  • miriammagallon (15)
Top Labels
Issue Labels
bug (3) enhancement (2) Usage Question (2)
Pull Request Labels
enhancement (2)

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 14,241 total
  • Total dependent packages: 2
  • Total dependent repositories: 0
  • Total versions: 6
  • Total maintainers: 1
bioconductor.org: CopyNumberPlots

Create Copy-Number Plots using karyoploteR functionality

  • Versions: 6
  • Dependent Packages: 2
  • Dependent Repositories: 0
  • Downloads: 14,241 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 21.8%
Downloads: 65.4%
Maintainers (1)
bgel@igtp.cat
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.6 depends
  • karyoploteR * depends
  • GenomeInfoDb * imports
  • GenomicRanges * imports
  • IRanges * imports
  • Rsamtools * imports
  • SummarizedExperiment * imports
  • VariantAnnotation * imports
  • cn.mops * imports
  • methods * imports
  • regioneR * imports
  • rhdf5 * imports
  • stats * imports
  • utils * imports
  • BSgenome.Hsapiens.UCSC.hg19.masked * suggests
  • BiocStyle * suggests
  • DNAcopy * suggests
  • knitr * suggests
  • panelcn.mops * suggests
  • rmarkdown * suggests
  • testthat * suggests