MetabolomicsBasics
Basic Functions to Investigate Metabolomics Data Matrices
Science Score: 23.0%
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
Found 1 DOI reference(s) in README -
✓Academic publication links
Links to: springer.com -
○Academic email domains
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○Scientific vocabulary similarity
Low similarity (14.6%) to scientific vocabulary
Last synced: 11 months ago
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JSON representation
Repository
Basic Functions to Investigate Metabolomics Data Matrices
Basic Info
- Host: GitHub
- Owner: janlisec
- Language: R
- Default Branch: master
- Size: 198 KB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Created almost 3 years ago
· Last pushed over 2 years ago
Metadata Files
Readme
README.Rmd
---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# MetabolomicsBasics
[](https://github.com/janlisec/MetabolomicsBasics/actions/workflows/R-CMD-check.yaml)
[](https://CRAN.R-project.org/package=MetabolomicsBasics)
The goal of MetabolomicsBasics is to provide a set of functions to investigate
raw data (a matrix of intensity values) from (metabol)omics experiments, i.e.
following peak picking and signal deconvolution.
Functions can be used to *i.e.*:
- normalize data
- detect biomarkers
- perform sample classification
A detailed description of best practice usage may be found in
the publication .
## Installation
You can install the development version of MetabolomicsBasics from [GitHub](https://github.com/) with:
``` r
# install.packages("devtools")
devtools::install_github("janlisec/MetabolomicsBasics")
```
## Examples
A typical use case would be to compute a Principal Component Analysis:
```{r example1, out.width="100%", fig.asp=1}
raw <- MetabolomicsBasics::raw
sam <- MetabolomicsBasics::sam
MetabolomicsBasics::RestrictedPCA(dat = raw, sam = sam, group.col = "Group", legend.x = "bottomleft", medsd = TRUE, fmod = "Group")
```
More elaborate plots, like the polar coordinate visualization of heterosis pattern are possible:
```{r example2, out.width="100%", fig.asp=1}
x <- t(raw)
colnames(x) <- sam$GT
MetabolomicsBasics::PolarCoordHeterPlot(x=x, gt=c("B73","B73xMo17","Mo17"), plot_lab="graph", col=1:10, thr=0.5, rev_log=exp(1))
```
Owner
- Name: JaLi
- Login: janlisec
- Kind: user
- Repositories: 1
- Profile: https://github.com/janlisec
GitHub Events
Total
Last Year
Packages
- Total packages: 1
-
Total downloads:
- cran 284 last-month
- Total docker downloads: 21,613
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 7
- Total maintainers: 1
cran.r-project.org: MetabolomicsBasics
Basic Functions to Investigate Metabolomics Data Matrices
- Homepage: https://github.com/janlisec/MetabolomicsBasics
- Documentation: http://cran.r-project.org/web/packages/MetabolomicsBasics/MetabolomicsBasics.pdf
- License: GPL-3
-
Latest release: 1.4.5
published over 2 years ago
Rankings
Dependent packages count: 29.8%
Dependent repos count: 35.5%
Average: 35.5%
Downloads: 41.2%
Maintainers (1)
Last synced:
about 1 year ago
Dependencies
.github/workflows/R-CMD-check.yaml
actions
- actions/checkout v3 composite
- r-lib/actions/check-r-package v2 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION
cran
- R >= 2.10.0 depends
- C50 * imports
- InterpretMSSpectrum * imports
- caret * imports
- e1071 * imports
- pcaMethods * imports
- plyr * imports
- rlang * imports
- rpart * imports
- webchem * imports
- mixOmics * suggests
- ropls * suggests
- xcms * suggests