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scinsight

Matrix factorization model for interpreting single cell gene expression in biologically heterogeneous data

https://github.com/vivianstats/scinsight

Science Score: 10.0%

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
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 2 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.7%) to scientific vocabulary

Keywords

bioinformatics gene-expression integration scrna-seq
Last synced: 6 months ago · JSON representation

Repository

Matrix factorization model for interpreting single cell gene expression in biologically heterogeneous data

Basic Info
Statistics
  • Stars: 19
  • Watchers: 1
  • Forks: 2
  • Open Issues: 7
  • Releases: 0
Topics
bioinformatics gene-expression integration scrna-seq
Created almost 5 years ago · Last pushed almost 2 years ago
Metadata Files
Readme

README.Rmd 

---
title: "scINSIGHT for interpreting single cell gene expression in biologically heterogeneous data"
author: "Kun Qian, Wei Vivian Li"

date: "`r Sys.Date()`"
output: github_document
---



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



## Latest News

> 2022/05/19:

 + Version 0.1.4 released!

 
## Introduction

scINSIGHT uses a novel matrix factorization model to jointly analyze multiple single-cell gene expression samples from biologically heterogeneous sources, such as different disease phases, treatment groups, or developmental stages. It assumes that each gene module is a sparse and non-negative linear combination of genes, and each cell is jointly defined by the expression of common and condition-specific modules.  Given multiple gene expression samples from different biological conditions, scINSIGHT aims to simultaneously identify common and condition-specific gene modules and quantify their expression levels in each sample in a lower-dimensional space.

Any suggestions on the package are welcome! For technical problems, please report to [Issues](https://github.com/Vivianstats/scINSIGHT/issues). For suggestions and comments on the method, please contact Kun () or Vivian (). 

## Installation

You can install `scINSIGHT` from [CRAN](https://cran.r-project.org/web/packages/scINSIGHT/index.html) with:

```{r gh-installation, eval = FALSE}
install.packages("scINSIGHT")
```

## Usage
Please refer to the [package vignette](https://github.com/Vivianstats/scINSIGHT/wiki/scINSIGHT-vignette) for examples about how to use the package functions.

Owner

  • Name: Vivian Li Lab
  • Login: Vivianstats
  • Kind: user
  • Company: University of California, Riverside

Statistical and bioinformatics methods developed by the Wei Vivian Li Lab.

GitHub Events

Total
  • Issues event: 1
  • Watch event: 2
  • Issue comment event: 3
  • Fork event: 1
Last Year
  • Issues event: 1
  • Watch event: 2
  • Issue comment event: 3
  • Fork event: 1

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 11
  • Total Committers: 2
  • Avg Commits per committer: 5.5
  • Development Distribution Score (DDS): 0.364
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Kun Qian s****k@g****m 7
Wei Vivian Li l****w@u****u 4
Committer Domains (Top 20 + Academic)
ucla.edu: 1

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 10
  • Total pull requests: 0
  • Average time to close issues: 13 days
  • Average time to close pull requests: N/A
  • Total issue authors: 8
  • Total pull request authors: 0
  • Average comments per issue: 1.7
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 0
  • Average time to close issues: about 1 hour
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • 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
View more stats
Top Authors
Issue Authors
  • XinyeZhao (2)
  • jeprob (2)
  • jmuribes (1)
  • aboutfanfan (1)
  • JahanRahman (1)
  • ERIGR (1)
  • YingboHuang (1)
  • nadinegheziel (1)
  • zyb1984 (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 270 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
cran.r-project.org: scINSIGHT

Interpretation of Heterogeneous Single-Cell Gene Expression Data

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 270 Last month
Rankings
Stargazers count: 13.3%
Forks count: 21.9%
Dependent packages count: 29.8%
Average: 32.4%
Dependent repos count: 35.5%
Downloads: 61.6%
Maintainers (1)
Kun_Qian@foxmail.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • methods * depends
  • RANN * imports
  • Rcpp * imports
  • igraph * imports
  • parallel * imports
  • stats * imports
  • stringr * imports