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EWCE

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

https://github.com/nathanskene/ewce

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
  • ✓
    Committers with academic emails
    4 of 12 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (17.8%) to scientific vocabulary

Keywords

deconvolution single-cell single-cell-rna-seq transcriptomics

Keywords from Contributors

bioconductor-package genomics genes ontologies sequencing clusters vcf-files summary-statistics standardisation qtl
Last synced: 6 months ago · JSON representation

Repository

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

Basic Info
Statistics
  • Stars: 57
  • Watchers: 4
  • Forks: 26
  • Open Issues: 10
  • Releases: 1
Topics
deconvolution single-cell single-cell-rna-seq transcriptomics
Created over 8 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog

README.Rmd 

---
title: "`EWCE`: `E`xpression `W`eighted `C`elltype `E`nrichment"
author: "`r rworkflows::use_badges(add_bioc_release = TRUE, add_bioc_download_month = TRUE, add_bioc_download_rank = TRUE, add_bioc_download_total = TRUE)`" 
date: "
README updated: `r format( Sys.Date(), '%b-%d-%Y')`
"
bibliography: inst/cit/EWCE.bib
csl: inst/cit/nature.csl
output: 
  github_document
---



```{r setup, echo=FALSE, include=FALSE}
pkg <- read.dcf("DESCRIPTION", fields = "Package")[1]
title <- read.dcf("DESCRIPTION", fields = "Title")[1]
description <- read.dcf("DESCRIPTION", fields = "Description")[1]
URL <- read.dcf('DESCRIPTION', fields = 'URL')[1]
owner <- strsplit(URL,"/")[[1]][4]
repo <- strsplit(URL,"/")[[1]][5]
```
 

## Introduction

The *EWCE* R package is designed to facilitate expression weighted cell type
enrichment analysis as described in our *Frontiers in Neuroscience* 
paper [@skene_2016]. *EWCE* can be applied to any gene list. 
 
Using *EWCE* essentially involves two steps:

1. Prepare a single-cell reference; i.e. CellTypeDataset (CTD). Alternatively, 
you can use one of the pre-generated CTDs we provide via the package `ewceData`
(which comes with *EWCE*).  
2. Run cell type enrichment on a user-provided gene list.

## Installation

*EWCE* requires [`R>=4.1`](https://www.r-project.org/) 
and `Bioconductor>=3.14`. 
To install *EWCE* on Bioconductor run:

```{r, eval=FALSE}
if (!require("BiocManager")){install.packages("BiocManager")}

BiocManager::install("EWCE") 
```

## Documentation 

### [Website](https://`r owner`.github.io/`r pkg`/)  

**NOTE**: This documentation is for the development version of ``r pkg``. See [Bioconductor](https://bioconductor.org/packages/release/bioc/html/EWCE.html) for documentation on the current release version.  

### [Getting started](https://`r owner`.github.io/`r pkg`/articles/`r pkg`)   

Includes:  

- A minimal example to get started with running *EWCE*. 
- How to install and use the dedicated *EWCE* Docker container usage. [Docker](https://www.docker.com/) containers with the latest version of `EWCE` 
are regularly pushed to 
[Dockerhub](https://hub.docker.com/repository/docker/neurogenomicslab/ewce).  

### [Extended examples](https://`r owner`.github.io/`r pkg`/articles/extended.html)

Additional tutorials of various *EWCE* features, including how to:  

- Run cell-type enrichment tests 
- Create a CellTypeDataset
- Merge two single-cell datasets 
- Run conditional cell-type enrichment tests
- Apply to transcriptomic data
 
## Updates

Major upgrades to *EWCE* were made in version 1.3.1.
Please see the [NEWS page](https://nathanskene.github.io/EWCE/news/index.html) for more details. 

## Troubleshooting

If you have any problems, please do submit an [Issue here on GitHub](https://github.com/nathanskene/EWCE/issues) with a reproducible example.

## Citation

If you use ``r pkg``, please cite: 


> `r citation(pkg)$textVersion`

If you use the cortex/hippocampus single-cell data associated 
*EWCE*/*ewceData* this package then please cite the following:

> [Zeisel, et al. Cell types in the mouse cortex and
hippocampus revealed by single-cell RNA-seq. Science, 2015.
](https://doi.org/10.1126/science.aaa1934)


 

## Contact
 
### [Neurogenomics Lab](https://www.neurogenomics.co.uk/)

UK Dementia Research Institute  
Department of Brain Sciences  
Faculty of Medicine  
Imperial College London   
[GitHub](https://github.com/neurogenomics)  
[DockerHub](https://hub.docker.com/orgs/neurogenomicslab)  

## References

Owner

  • Name: Nathan Skene
  • Login: NathanSkene
  • Kind: user
  • Location: London, UK

UK DRI Group Leader & UKRI Future Leaders Fellow at Imperial College Dementia Research Institute

GitHub Events

Total
  • Issues event: 2
  • Watch event: 3
  • Issue comment event: 6
  • Push event: 4
  • Fork event: 1
  • Create event: 1
Last Year
  • Issues event: 2
  • Watch event: 3
  • Issue comment event: 6
  • Push event: 4
  • Fork event: 1
  • Create event: 1

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 265
  • Total Committers: 12
  • Avg Commits per committer: 22.083
  • Development Distribution Score (DDS): 0.653
Past Year
  • Commits: 4
  • Committers: 2
  • Avg Commits per committer: 2.0
  • Development Distribution Score (DDS): 0.5
Top Committers
Name Email Commits
Brian M. Schilder 3****r 92
Al-Murphy a****4@h****m 85
Nathan Skene n****e@i****k 34
nskene n****e@g****m 14
NathanSkene n****e@k****e 11
J Wokaty j****y@s****u 10
Nathan Skene 3****e 8
Nitesh Turaga n****a@g****m 6
ovrhuman 7****n 2
nfancy 5****y 1
Emir Turkes e****s@b****u 1
Alan E Murphy a****y@l****k 1
Committer Domains (Top 20 + Academic)
login-7.rcs.ic.ac.uk: 1 bu.edu: 1 sph.cuny.edu: 1 ki.se: 1 ic.ac.uk: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 87
  • Total pull requests: 9
  • Average time to close issues: 4 months
  • Average time to close pull requests: 16 days
  • Total issue authors: 33
  • Total pull request authors: 5
  • Average comments per issue: 2.59
  • Average comments per pull request: 2.22
  • Merged pull requests: 8
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 0
  • Average time to close issues: N/A
  • 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
  • bschilder (23)
  • NathanSkene (18)
  • h1hui (5)
  • Al-Murphy (5)
  • alexandruioanvoda (3)
  • iscastanho (2)
  • SuMi300 (2)
  • rbutleriii (2)
  • forrestzhaosen (2)
  • KevinMarinus (2)
  • Kfarls (1)
  • tkamath1 (1)
  • roxyisat-rex (1)
  • artemisiat (1)
  • kvshams (1)
Pull Request Authors
  • NathanSkene (4)
  • bschilder (2)
  • eturkes (1)
  • nfancy (1)
  • bobGSmith (1)
Top Labels
Issue Labels
bug (21) enhancement (8) benchmarking (5) GitHub Actions (2) question (1) good first issue (1) invalid (1)
Pull Request Labels
enhancement (1)

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 16,586 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 6
  • Total maintainers: 1
bioconductor.org: EWCE

Expression Weighted Celltype Enrichment

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 16,586 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 21.3%
Downloads: 63.9%
Maintainers (1)
alanmurph94@hotmail.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.2 depends
  • RNOmni >= 1.0 depends
  • BiocParallel * imports
  • DelayedArray * imports
  • HGNChelper * imports
  • Matrix * imports
  • SingleCellExperiment * imports
  • SummarizedExperiment * imports
  • data.table * imports
  • dplyr * imports
  • ewceData * imports
  • ggplot2 * imports
  • limma * imports
  • methods * imports
  • orthogene >= 0.99.8 imports
  • parallel * imports
  • reshape2 * imports
  • stats * imports
  • stringr * imports
  • utils * imports
  • BiocStyle * suggests
  • DESeq2 * suggests
  • DelayedMatrixStats * suggests
  • MAST * suggests
  • badger * suggests
  • cowplot * suggests
  • ggdendro * suggests
  • grDevices * suggests
  • grid * suggests
  • gridExtra * suggests
  • knitr * suggests
  • magick * suggests
  • markdown * suggests
  • memoise * suggests
  • readxl * suggests
  • remotes * suggests
  • rmarkdown * suggests
  • scales * suggests
  • sctransform * suggests
  • testthat >= 3.0.0 suggests
.github/workflows/check-bioc-docker.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact v2 composite
  • docker/build-push-action v1 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
Dockerfile docker
  • bioconductor/bioconductor_docker devel build