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Open Source Science

https://github.com/campbio/decontx

Methods for decontamination of single cell data

https://github.com/campbio/decontx

Science Score: 36.0%

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
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: biorxiv.org
  • ○
    Academic email domains
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.8%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Methods for decontamination of single cell data

Basic Info
  • Host: GitHub
  • Owner: campbio
  • License: mit
  • Language: R
  • Default Branch: main
  • Size: 13.7 MB
Statistics
  • Stars: 37
  • Watchers: 2
  • Forks: 3
  • Open Issues: 0
  • Releases: 3
Created over 3 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License

README.Rmd 

---
output: github_document
---



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

# decontX


[![R-CMD-check](https://github.com/campbio/decontX/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/campbio/decontX/actions/workflows/R-CMD-check.yaml)
[![codecov](https://codecov.io/gh/campbio/decontX/graph/badge.svg?token=z5YnsXuWqh)](https://codecov.io/gh/campbio/decontX)


Methods for decontamination of single cell data. This package implements both DecontX (Yang et al., [2020](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-1950-6)) for single-cell RNA-seq data and DecontPro (Yin et al., [2023](https://www.biorxiv.org/content/10.1101/2023.01.27.525964v2)) for single-cell protein expression data.

## Installation Instructions

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

```r
# install.packages("devtools")
devtools::install_github("campbio/decontX")
```

## Vignettes

To build vignette when installing from GitHub:

``` {r eval=FALSE}
library(devtools)
install_github("campbio/decontX", build_vignettes = TRUE)
```

Vignettes can be accessed through:

```{r eval=FALSE}
vignette('decontX', package = 'decontX')
vignette('decontPro', package = 'decontX')
```

Owner

  • Name: campbio
  • Login: campbio
  • Kind: organization

GitHub Events

Total
  • Issues event: 5
  • Watch event: 16
  • Issue comment event: 5
  • Push event: 9
  • Pull request event: 4
  • Fork event: 3
  • Create event: 1
Last Year
  • Issues event: 5
  • Watch event: 16
  • Issue comment event: 5
  • Push event: 9
  • Pull request event: 4
  • Fork event: 3
  • Create event: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 3
  • Total pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 3
  • Total pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 3
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
  • Reyhaneh92 (1)
  • YMSen (1)
  • Sirin24 (1)
  • kimyoki123 (1)
  • ccrobertson (1)
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Pull Request Authors
  • andrjohns (1)
  • Goultard59 (1)
  • yuan-yin-truly (1)
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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/test-coverage.yaml actions
  • actions/checkout v3 composite
  • actions/upload-artifact v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • R >= 3.4.0 depends
  • DelayedArray * imports
  • MCMCprecision * imports
  • Matrix >= 1.5.3 imports
  • Rcpp >= 0.12.0 imports
  • RcppParallel >= 5.0.1 imports
  • S4Vectors * imports
  • Seurat * imports
  • SingleCellExperiment * imports
  • SummarizedExperiment * imports
  • celda * imports
  • dbscan * imports
  • ggplot2 * imports
  • methods * imports
  • patchwork * imports
  • plyr * imports
  • reshape2 * imports
  • rstan >= 2.18.1 imports
  • rstantools >= 2.2.0 imports
  • scater * imports
  • withr * imports
  • BiocStyle * suggests
  • SingleCellMultiModal * suggests
  • TENxPBMCData * suggests
  • dplyr * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • scran * suggests
  • testthat >= 3.0.0 suggests