https://github.com/almaaslab/micint
R package for analyzing microbial co-occurences
Science Score: 10.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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○DOI references
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✓Academic publication links
Links to: nature.com -
○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (9.9%) to scientific vocabulary
Keywords
Repository
R package for analyzing microbial co-occurences
Statistics
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
Overview
micInt is an R package designed for analyzing microbial co-occurences. It takes in OTU tables was either pure dataFrames or as experiment-level phyloseq objects. Roughly, the package is composed of three major parts:
* CoNet-based analysis of pairwise co-occurences. Primary functions: runAnalysis (high level) and ccrepe (low level)
* Lotka-Volterra modelling of time dynamics. Primary functions: integralSystem, cv.LV and ridge_fit
* Utility functions, includes refine_data, subset_by_environment, similarity_measures and scale_by_column.
Install
This package have the following dependencies which must be installed prior to installing this package:
From CRAN:
* infotheo
* matrixStats
* magrittr
* deSolve
* igraph
* dplyr
* rlang
* glue
* viridis
* RhpcBLASctl
* ggplot2
* ggfortify
From Bioconductor:
* phyloseq
If all dependencies are satisfied, the package can we installed from GitHub as follows:
install.packages("devtools")
library(devtools)
install_github("AlmaasLab/micInt")
For a quit start automatically installing all dependencies, consider:
install.packages("BiocManager","devtools")
devtools::install_github("AlmaasLab/micInt",repos=BiocManager::BiocManager::repositories())
Useage
Please read the article "Robust bacterial co-occurence community structures are independent of r- and K-selection history" (https://www.nature.com/articles/s41598-021-03018-z) where this package is used. The source code for the article is available on https://github.com/yaccos/Microbial-co-occurence.
Unfortunately, I have not yet taken the effort to write a proper vignette. However, if you are interested in using the package, don`t hasitate asking me for help, either as a github issue or directly (jakob.p.pettersen@ntnu.no).
Owner
- Name: AlmaasLab
- Login: AlmaasLab
- Kind: organization
- Email: eivind.almaas@ntnu.no
- Location: Trondheim, Norway
- Website: http://www.ntnu.edu/almaaslab
- Repositories: 4
- Profile: https://github.com/AlmaasLab
Network Systems Biology
GitHub Events
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- Watch event: 1
Dependencies
- actions/cache v2 composite
- actions/checkout v2 composite
- actions/upload-artifact master composite
- r-lib/actions/setup-pandoc master composite
- r-lib/actions/setup-r master composite
- r-lib/actions/setup-tinytex v1 composite
- R >= 3.5.0 depends
- ggfortify * depends
- ggplot2 * depends
- RhpcBLASctl * imports
- deSolve * imports
- dplyr * imports
- glue * imports
- igraph * imports
- infotheo * imports
- magrittr * imports
- matrixStats * imports
- methods * imports
- parallel * imports
- phyloseq * imports
- rlang * imports
- tibble * imports
- utils * imports
- vegan * imports
- viridis * imports
- BiocStyle * suggests
- cluster * suggests
- covr * suggests
- ggdendro * suggests
- ggrepel * suggests
- kableExtra * suggests
- knitr * suggests
- readxl * suggests
- testthat * suggests