scploidy

https://github.com/fumi-github/scploidy

Science Score: 26.0%

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Found 4 DOI reference(s) in README
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Low similarity (9.1%) to scientific vocabulary

Last synced: 10 months ago · JSON representation

Repository

Basic Info

Host: GitHub
Owner: fumi-github
License: other
Language: R
Default Branch: main
Size: 2.99 MB

Statistics

Stars: 3
Watchers: 1
Forks: 2
Open Issues: 3
Releases: 0

Created almost 4 years ago · Last pushed almost 2 years ago

Metadata Files

Readme License

scPloidy

scPloidy is an R package to compute ploidy of single cells (or nuclei) based on single-cell (or single-nucleus) ATAC-seq data. In ATAC-seq, open chromatin regions are excised and sequenced. For any site on the genome, ATAC-seq could read 0, 1 or 2 DNA fragments, if the cell was diploid. If the cell was tetraploid, ATAC-seq could read 0, 1, 2, 3 or 4 fragments from the same site. This is the basic idea used in scPloidy. We model the depth of DNA sequencing at one site by binomial distribution. Additionally, this method can be adapted to detect the proliferating stage in the cell cycle and copy number variations in cancer cells.

The algorithm should also work for single-cell (or single-nucleus) whole genome sequencing, if the template DNA is tagmented first. It does not work for whole genome amplified DNA.

This is published in Genetics. Related data is available from figshare.

scPloidy can also be used for detecting multiplets (doublets, triplets) in single-cell assay. Based on biological knowledge, if the cells in your sample are likely all diploids, you can regard the detected polyploid cells as multiplets. Indeed, scPloidy can detect aggregation of cells of the same cell type, which cannot be detected by RNA-seq based algorithms (e.g., Scrublet, DoubletFinder, DoubletDecon).

Questions? Please submit to GitHub Issues or e-mail fumihiko AT takeuchi DOT name

Installation in R

Beforehand, these packages need to be installed from Bioconductor:

if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install(c("GenomicRanges", "IRanges", "Rsamtools"))

Install from CRAN:

install.packages('scPloidy')

In order to install the developmental version:

install.packages('devtools')
devtools::install_github('fumi-github/scPloidy', build_vignettes = TRUE)

To uninstall package:

remove.packages('scPloidy')

Usage

library(scPloidy)
vignette('intro', package = 'scPloidy')

Owner

Login: fumi-github
Kind: user

Repositories: 3
Profile: https://github.com/fumi-github

GitHub Events

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Issues event: 1

Last Year

Issues event: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time

Total issues: 3
Total pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Total issue authors: 2
Total 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

Past Year

Issues: 1
Pull requests: 0
Average time to close issues: N/A
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

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Top Authors

Issue Authors

fumi-github (2)
Mervyn010 (1)

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Packages

Total packages: 1
Total downloads:
- cran 591 last-month
Total docker downloads: 48

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 2
Total maintainers: 1

cran.r-project.org: scPloidy

Infer Ploidy of Single Cells

Documentation: http://cran.r-project.org/web/packages/scPloidy/scPloidy.pdf
License: MIT + file LICENSE
Latest release: 0.6.2
published about 2 years ago

Versions: 2
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 591 Last month
Docker Downloads: 48

Rankings

Forks count: 21.9%

Stargazers count: 28.5%

Dependent packages count: 29.8%

Dependent repos count: 35.5%

Average: 38.8%

Downloads: 78.5%

Maintainers (1)

fumihiko@takeuchi.name