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ccdf

Distribution-Free Single-cell Differential Expression Analysis

https://github.com/mgauth/ccdf

Science Score: 23.0%

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    Found 3 DOI reference(s) in README
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    2 of 3 committers (66.7%) from academic institutions
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    Low similarity (13.9%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Distribution-Free Single-cell Differential Expression Analysis

Basic Info
  • Host: GitHub
  • Owner: Mgauth
  • License: gpl-3.0
  • Language: R
  • Default Branch: main
  • Homepage:
  • Size: 339 KB
Statistics
  • Stars: 1
  • Watchers: 3
  • Forks: 2
  • Open Issues: 1
  • Releases: 0
Created over 5 years ago · Last pushed over 4 years ago
Metadata Files
Readme License

README.Rmd 

---
output: github_document
---



```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)
```

# `ccdf`

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

## Overview

`ccdf` is a package for performing single-cell RNA-seq differential expression analysis and more generally **complex hypothesis testing**. 

The main function of the package is `ccdf_testing()`. It  allows to use either an asymptotic test for large sample size or a permutation test for small sample size with the argument `method`.

The methods implemented in this package are detailed in the following article:

> Gauthier M, Agniel D, Thiébaut R & Hejblum BP (2020). Distribution-free complex hypothesis testing for single-cell RNA-seq differential expression analysis, *BioRxiv*  [doi:10.1101/2021.05.21.445165](https://doi.org/10.1101/2021.05.21.445165)



## Installation


**`ccdf` is available from CRAN.**
```{r CRAN-install, eval=FALSE}
install.packages("ccdf")
```


**To install `ccdf`, you can download the development version on [GitHub](https://github.com/Mgauth/ccdf).**
```{r GitHub-install, eval=FALSE}
#install.packages("devtools")
devtools::install_github("Mgauth/ccdf")
```


## Example

Here is a basic example which shows how to use `ccdf` with simple generated data.

```{r example, eval = FALSE}
## Data Generation
X <- data.frame("X1" = as.factor(rbinom(n=100, size = 1, prob = 0.5)))
Y <- data.frame("gene1" = t(replicate(10, ((X$X1==1)*rnorm(n = 50,0,1)) + ((X$X1==0)*rnorm(n = 50,0.5,1)))))
```

```{r estimation, eval = FALSE}
# Hypothesis testing
res_asymp <- ccdf_testing(exprmat=Y, variable2test=X, test="asymptotic") # asymptotic test
res_perm <- ccdf_testing(exprmat=Y, variable2test=X, test="permutations",
                         adaptive=TRUE) # adaptive permutation test
```


 -- Marine Gauthier, Denis Agniel, Rodolphe Thiébaut & Boris Hejblum

GitHub Events

Total
Last Year

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 137
  • Total Committers: 3
  • Avg Commits per committer: 45.667
  • Development Distribution Score (DDS): 0.19
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Marine Gauthier m****r@u****r 111
Mgauth 3****h 22
borishejblum b****m@u****r 4
Committer Domains (Top 20 + Academic)
u-bordeaux.fr: 2

Issues and Pull Requests

Last synced: almost 3 years ago

All Time
  • Total issues: 2
  • Total pull requests: 0
  • Average time to close issues: 22 days
  • Average time to close pull requests: N/A
  • Total issue authors: 2
  • Total pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • 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
  • NadineBestard (1)
  • Mgauth (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads: unknown
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 1
  • Total maintainers: 1
cran.r-project.org: ccdf

Distribution-Free Single-Cell Differential Expression Analysis

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Forks count: 21.9%
Average: 29.7%
Dependent packages count: 29.8%
Stargazers count: 31.7%
Dependent repos count: 35.5%
Maintainers (1)
marine.gauthier@u-bordeaux.fr
Last synced: almost 3 years ago

Dependencies

DESCRIPTION cran
  • R >= 3.6 depends
  • CompQuadForm * imports
  • RcppNumerical * imports
  • cowplot * imports
  • doParallel * imports
  • foreach * imports
  • ggplot2 * imports
  • matrixStats * imports
  • parallel * imports
  • pbapply * imports
  • randomForest * imports
  • rpart * imports
  • statmod * imports
  • survey * imports
  • viridisLite * imports