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MicrobiomeProfiler

:microbe: A shiny package for microbiome functional enrichment analysis

https://github.com/yulab-smu/microbiomeprofiler

Science Score: 49.0%

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
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 7 committers (14.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (5.1%) to scientific vocabulary

Keywords from Contributors

bioconductor-packages immune-repertoire gene grna-sequence sequencing ontologies genomics microbiome-analysis microbiome-data microbiome
Last synced: 7 months ago · JSON representation

Repository

:microbe: A shiny package for microbiome functional enrichment analysis

Basic Info
Statistics
  • Stars: 37
  • Watchers: 3
  • Forks: 8
  • Open Issues: 1
  • Releases: 0
Created over 4 years ago · Last pushed 12 months ago
Metadata Files
Readme Changelog

README.md

Introduction

MicrobiomeProfiler is an R-shiny package based on clusterProfiler, is user-friendly tool for functional enrichment analysis in microbiome data (T Wu, et al., 2021).

Installation

Installation via BiocManager:

if (!require("BiocManager"))
    install.packages("BiocManager")
BiocManager::install("MicrobiomeProfiler")

Or install MicrobiomeProfiler from github using devtools :

## Note that having installed clusterProfiler,config,DT,enrichplot,golem,magrittr,shiny,shinyWidgets,shinycustomloader,htmltools,ggplot2
if (!requireNamespace("devtools", quietly=TRUE))
    install.packages("devtools")
devtools::install_github("YuLab-SMU/MicrobiomeProfiler")

Quick Guides

library(MicrobiomeProfiler)
run_MicrobiomeProfiler()

Reference

  • T Wu#, E Hu#, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo*, G Yu*. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. The Innovation. 2021, 2(3):100141. doi: 10.1016/j.xinn.2021.100141

Owner

  • Name: Bioinformatics Group @ SMU
  • Login: YuLab-SMU
  • Kind: organization
  • Email: gcyu1@smu.edu.cn
  • Location: Guangzhou

Research group led by Prof. Guangchuang Yu in School of Basic Medical Sciences, Southern Medical University

GitHub Events

Total
  • Watch event: 2
  • Push event: 2
  • Fork event: 1
Last Year
  • Watch event: 2
  • Push event: 2
  • Fork event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 65
  • Total Committers: 7
  • Avg Commits per committer: 9.286
  • Development Distribution Score (DDS): 0.323
Past Year
  • Commits: 18
  • Committers: 5
  • Avg Commits per committer: 3.6
  • Development Distribution Score (DDS): 0.667
Top Committers
Name Email Commits
mjchen1996 m****6@o****m 44
Guangchuang Yu g****u@g****m 6
Nitesh Turaga n****a@g****m 4
J Wokaty j****y@s****u 4
mjchen1996 m****6@o****m 3
xiangpin x****n@1****m 2
J Wokaty j****y 2
Committer Domains (Top 20 + Academic)
163.com: 1 outloo.com: 1 sph.cuny.edu: 1

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 8,810 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: MicrobiomeProfiler

An R/shiny package for microbiome functional enrichment analysis

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 8,810 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Stargazers count: 5.6%
Forks count: 10.0%
Average: 20.4%
Downloads: 86.6%
Maintainers (1)
guangchuangyu@gmail.com
Last synced: 7 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.1.0 depends
  • DT * imports
  • clusterProfiler >= 4.5.2 imports
  • config * imports
  • enrichplot * imports
  • ggplot2 * imports
  • golem * imports
  • graphics * imports
  • gson * imports
  • htmltools * imports
  • magrittr * imports
  • shiny >= 1.6.0 imports
  • shinyWidgets * imports
  • shinycustomloader * imports
  • stats * imports
  • utils * imports
  • knitr * suggests
  • rmarkdown * suggests
  • testthat >= 3.0.0 suggests