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karyotapr

CNV Analysis for Tapestri

https://github.com/joeymays/karyotapr

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 1 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: biorxiv.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.5%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

CNV Analysis for Tapestri

Basic Info
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 1
  • Open Issues: 0
  • Releases: 2
Created almost 4 years ago · Last pushed about 2 years ago
Metadata Files
Readme License

README.Rmd 

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# karyotapR


[![R-CMD-check](https://github.com/joeymays/karyotapR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/joeymays/karyotapR/actions/workflows/R-CMD-check.yaml)
[![CRAN status](https://www.r-pkg.org/badges/version/karyotapR)](https://CRAN.R-project.org/package=karyotapR)


karyotapR enables analysis of DNA copy number (aneuploidy) using data produced by the KaryoTap method. Users can easily parse, manipulate, and visualize datasets produced from the automated 'Tapestri Pipeline', with support for normalization, clustering, and copy number calling. Functions are also available to deconvolute multiplexed samples by genotype and parsing barcoded reads from exogenous lentiviral constructs.

KaryoTap combines custom genome-wide targeted DNA sequencing panels for the Mission Bio Tapestri system with a Gaussian mixture model framework for calling copy number.

## References

Mays JC et al., 2023. _KaryoTap Enables Aneuploidy Detection in Thousands of Single Human Cells._ https://www.biorxiv.org/content/10.1101/2023.09.08.555746v1. 

## Installation

You can install the current stable version of karyotapR from
[CRAN](https://cran.r-project.org/package=karyotapR) with:

```r
install.packages('karyotapR')
```

You can install the development version of karyotapR from [GitHub](https://github.com/joeymays/karyotapR) with:

``` r
# install.packages("devtools")
devtools::install_github("joeymays/karyotapR")
```

## Workflow

For details on the workflow, see the [Getting Started](https://joeymays.xyz/karyotapR/articles/karyotapR.html) guide, articles on this site, and the package reference/documentation.

![](https://joeymays.xyz/workflow.png)

Owner

  • Name: Joey Mays
  • Login: joeymays
  • Kind: user

PhD Candidate at NYU School of Medicine

GitHub Events

Total
  • Fork event: 2
Last Year
  • Fork event: 2

Packages

  • Total packages: 1
  • Total downloads:
    • cran 206 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 1
  • Total maintainers: 1
cran.r-project.org: karyotapR

DNA Copy Number Analysis for Genome-Wide Tapestri Panels

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 206 Last month
Rankings
Forks count: 28.2%
Dependent packages count: 28.2%
Stargazers count: 34.9%
Dependent repos count: 36.7%
Average: 43.2%
Downloads: 87.9%
Maintainers (1)
josephcmays@gmail.com
Last synced: 11 months ago

Dependencies

.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • R >= 3.6 depends
  • SingleCellExperiment * depends
  • BiocGenerics * imports
  • ComplexHeatmap * imports
  • GenomicRanges * imports
  • IRanges * imports
  • S4Vectors * imports
  • SummarizedExperiment * imports
  • circlize * imports
  • dplyr * imports
  • ggplot2 * imports
  • gtools * imports
  • magrittr * imports
  • methods * imports
  • rhdf5 * imports
  • rlang * imports
  • stats * imports
  • tibble * imports
  • tidyr * imports
  • umap * imports
  • viridisLite * imports
  • Biostrings * suggests
  • Rsamtools * suggests
  • dbscan * suggests
  • testthat >= 3.0.0 suggests