Data

Tools

Indexes

Applications

Experiments

Open Source Science

reclanc

https://github.com/kaiaragaki/reclanc

Science Score: 39.0%

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 6 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.9%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 8
  • Releases: 0
Created about 2 years ago · Last pushed almost 2 years ago
Metadata Files
Readme Contributing License Codemeta

README.Rmd 

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# reclanc


[![codecov](https://codecov.io/gh/KaiAragaki/reclanc/branch/master/graph/badge.svg?token=Z1AquW3Awo)](https://codecov.io/gh/KaiAragaki/reclanc)


reclanc is a revival of [ClaNC (Classification of microarrays to nearest centroids), by Alan R. Dabney](https://doi.org/10.1093/bioinformatics/bti681).

Since the source has been lost (at least to my knowledge), the code comes from [here](https://github.com/naikai/sake/blob/master/R/clanc.R) with heavy modification.

reclanc is a nearest-centroid classifier for expression data. It tends to be a little more sensitive and accurate than similar models like PAM.

Besides its mere existence, reclanc differs slightly from the original ClaNC package in a few ways:

- reclanc supports a wide variety of inputs (`data.frame`, `matrix`, `formula`,  `recipe`, `ExpressionSet`, and `SummarizedExperiment`)
- reclanc plays nicely with [tidymodels](https://www.tidymodels.org/), and offloads things like making folds to `rsample` and tuning to `tune` (see [this vignette](https://kaiaragaki.github.io/reclanc/articles/case-study.html) for how to leverage tidymodels with reclanc). 
- Provides a prediction method based on correlation, rather than distance - useful for predicting classes from data from different sequencing modalities

## Installation

You can install the development version of reclanc like so:

``` r
# install.packages("pak")
pak::pak("KaiAragaki/reclanc")
```

## How to use it

```{r}
library(reclanc)
lapply(synthetic_expression, head) # dummy data
```

```{r}
centroids <- clanc(
  synthetic_expression$expression,
  classes = synthetic_expression$classes,
  active = 5
)
centroids
```

For information on basic usage, see [this](https://kaiaragaki.github.io/reclanc/articles/using-reclanc.html) vignette. For a case study, as well as how to optimize the `active` parameter, see [this](https://kaiaragaki.github.io/reclanc/articles/case-study.html) vignette.


## How it works

You can find a gentle introduction to how reclanc works [here](https://kai.rbind.io/posts/projects-reclanc/) and a more in-depth and statistically rigorous definition of how this algorithm works in the  [original paper](https://doi.org/10.1093/bioinformatics/bti681).

## Citation

Citation for the original ClaNC paper:

Alan R. Dabney, Classification of microarrays to nearest centroids, Bioinformatics, Volume 21, Issue 22, November 2005, Pages 4148–4154, https://doi.org/10.1093/bioinformatics/bti681

Owner

  • Name: Kai Aragaki
  • Login: KaiAragaki
  • Kind: user

whatever the exact opposite of an emotional support dog is

CodeMeta (codemeta.json) 

{
  "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
  "@type": "SoftwareSourceCode",
  "identifier": "reclanc",
  "description": "Classification of microarrays to nearest centroids (ClaNC) <doi:10.1093/bioinformatics/bti756> selects optimal genes for centroids, similar to Prediction Analysis for Microarrays (PAM) but using fewer corrective factors, resulting in greater sensitivity and accuracy. Unfortunately, the original source of ClaNC can no longer be found. 'reclanc' reimplements this algorithm, with the the additional benefit of increased interoperability with standard data structures and modeling ecosystems.",
  "name": "reclanc: A Revival of the ClaNC Algorithm",
  "relatedLink": "https://kaiaragaki.github.io/reclanc/",
  "codeRepository": "https://github.com/KaiAragaki/reclanc",
  "issueTracker": "https://github.com/KaiAragaki/reclanc/issues",
  "license": "https://spdx.org/licenses/MIT",
  "version": "0.0.0.9000",
  "programmingLanguage": {
    "@type": "ComputerLanguage",
    "name": "R",
    "url": "https://r-project.org"
  },
  "runtimePlatform": "R version 4.4.1 (2024-06-14)",
  "author": [
    {
      "@type": "Person",
      "givenName": "Kai",
      "familyName": "Aragaki",
      "email": "kaiaragaki@proton.me",
      "@id": "https://orcid.org/0000-0002-9458-0426"
    },
    {
      "@type": "Person",
      "givenName": "Alan",
      "familyName": "Dabney",
      "email": "adabney@stat.tamu.edu"
    }
  ],
  "copyrightHolder": [
    {
      "@type": "Person",
      "givenName": "Alan",
      "familyName": "Dabney",
      "email": "adabney@stat.tamu.edu"
    }
  ],
  "maintainer": [
    {
      "@type": "Person",
      "givenName": "Kai",
      "familyName": "Aragaki",
      "email": "kaiaragaki@proton.me",
      "@id": "https://orcid.org/0000-0002-9458-0426"
    }
  ],
  "softwareSuggestions": [
    {
      "@type": "SoftwareApplication",
      "identifier": "aws.s3",
      "name": "aws.s3",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=aws.s3"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "Biobase",
      "name": "Biobase",
      "provider": {
        "@id": "https://www.bioconductor.org",
        "@type": "Organization",
        "name": "Bioconductor",
        "url": "https://www.bioconductor.org"
      },
      "sameAs": "https://bioconductor.org/packages/release/bioc/html/Biobase.html"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "cellebrate",
      "name": "cellebrate",
      "sameAs": "https://github.com/McConkeyLab/cellebrate"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "knitr",
      "name": "knitr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=knitr"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "rmarkdown",
      "name": "rmarkdown",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=rmarkdown"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "SummarizedExperiment",
      "name": "SummarizedExperiment",
      "provider": {
        "@id": "https://www.bioconductor.org",
        "@type": "Organization",
        "name": "Bioconductor",
        "url": "https://www.bioconductor.org"
      },
      "sameAs": "https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "testthat",
      "name": "testthat",
      "version": ">= 3.0.0",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=testthat"
    },
    {
      "@type": "SoftwareApplication",
      "identifier": "tidymodels",
      "name": "tidymodels",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=tidymodels"
    }
  ],
  "softwareRequirements": {
    "1": {
      "@type": "SoftwareApplication",
      "identifier": "R",
      "name": "R",
      "version": ">= 4.1.0"
    },
    "2": {
      "@type": "SoftwareApplication",
      "identifier": "cli",
      "name": "cli",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=cli"
    },
    "3": {
      "@type": "SoftwareApplication",
      "identifier": "collapse",
      "name": "collapse",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=collapse"
    },
    "4": {
      "@type": "SoftwareApplication",
      "identifier": "dplyr",
      "name": "dplyr",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=dplyr"
    },
    "5": {
      "@type": "SoftwareApplication",
      "identifier": "hardhat",
      "name": "hardhat",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=hardhat"
    },
    "6": {
      "@type": "SoftwareApplication",
      "identifier": "parsnip",
      "name": "parsnip",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=parsnip"
    },
    "7": {
      "@type": "SoftwareApplication",
      "identifier": "recipes",
      "name": "recipes",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=recipes"
    },
    "8": {
      "@type": "SoftwareApplication",
      "identifier": "rlang",
      "name": "rlang",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=rlang"
    },
    "9": {
      "@type": "SoftwareApplication",
      "identifier": "stats",
      "name": "stats"
    },
    "10": {
      "@type": "SoftwareApplication",
      "identifier": "tibble",
      "name": "tibble",
      "provider": {
        "@id": "https://cran.r-project.org",
        "@type": "Organization",
        "name": "Comprehensive R Archive Network (CRAN)",
        "url": "https://cran.r-project.org"
      },
      "sameAs": "https://CRAN.R-project.org/package=tibble"
    },
    "SystemRequirements": null
  },
  "fileSize": "63.175KB",
  "readme": "https://github.com/KaiAragaki/reclanc/blob/master/README.md"
}

GitHub Events

Total
Last Year

Dependencies

DESCRIPTION cran
  • dplyr * imports
  • testthat >= 3.0.0 suggests