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rRDP

Seamlessly interfaces RDP classifier.

https://github.com/mhahsler/rrdp

Science Score: 23.0%

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
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    DOI references
  • ○
    Academic publication links
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    Committers with academic emails
    2 of 9 committers (22.2%) from academic institutions
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    Scientific vocabulary similarity
    Low similarity (10.5%) to scientific vocabulary

Keywords

bioconductor bioinformatics classification

Keywords from Contributors

bioconductor-package proteomics tracking particles microscopy fluorescence core-package mass-spectrometry peptides bioc
Last synced: 6 months ago · JSON representation

Repository

Seamlessly interfaces RDP classifier.

Basic Info
  • Host: GitHub
  • Owner: mhahsler
  • License: other
  • Language: R
  • Default Branch: devel
  • Homepage:
  • Size: 2.86 MB
Statistics
  • Stars: 3
  • Watchers: 2
  • Forks: 1
  • Open Issues: 0
  • Releases: 0
Topics
bioconductor bioinformatics classification
Created over 3 years ago · Last pushed almost 2 years ago
Metadata Files
Readme License

README.Rmd 

---
output: github_document
---



```{r echo=FALSE, results = 'asis'}
pkg <- "rRDP"

source("https://raw.githubusercontent.com/mhahsler/pkg_helpers/main/pkg_helpers.R")
pkg_title(pkg, CRAN = FALSE, Bioc = TRUE)
```

This package installs and interfaces the naive Bayesian classifier for 16S rRNA 
sequences developed by the Ribosomal Database Project (RDP). With this package the 
classifier trained with the standard training set can be used or a custom classifier can be trained.


Other R interfaces for bioinformatics are also available:

* [rBLAST](https://bioconductor.org/packages/rBLAST): Interface to the Basic Local Alignment Search Tool (BLAST) to search genetic sequence data bases 
* [rMSA](https://mhahsler.r-universe.dev/ui#package:rMSA): Interface for Popular Multiple 
    Sequence Alignment Tools including ClustalW, MAFFT, MUSCLE, and Kalign


## Installation

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

BiocManager::install("rRDP")
BiocManager::install("rRDPData")
```

## Usage

```{r, message=FALSE}
library(rRDP)
```

Load a few sequences and classify the sequences using RDP.

```{r}
seq <- readRNAStringSet(system.file("examples/RNA_example.fasta",
  package="rRDP"))
seq

pred <- predict(rdp(), seq)
pred

attr(pred, "confidence")
```


## Citation Request

```{r, echo=FALSE, results='asis', comment= ""}
pkg_citation(pkg)
```

## Acknowledgments
This work was partially supported by grant no. R21HG005912 from the [National Human Genome Research Institute](https://www.genome.gov/).

Owner

  • Name: Michael Hahsler
  • Login: mhahsler
  • Kind: user
  • Location: Dallas, TX
  • Company: SMU

I develop packages for AI, ML, and Data Science.

GitHub Events

Total
  • Watch event: 3
Last Year
  • Watch event: 3

Committers

Last synced: 10 months ago

All Time
  • Total Commits: 67
  • Total Committers: 9
  • Avg Commits per committer: 7.444
  • Development Distribution Score (DDS): 0.672
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Michael Hahsler m****r@s****u 22
Nitesh Turaga n****a@g****m 14
Dan Tenenbaum d****a@f****g 11
J Wokaty j****y@s****u 6
Hervé Pagès h****s@f****g 4
Herve Pages h****s@f****g 4
vobencha v****a@g****m 2
vobencha v****n@r****g 2
Marc Carlson m****n@f****g 2
Committer Domains (Top 20 + Academic)
fhcrc.org: 3 roswellpark.org: 1 fredhutch.org: 1 sph.cuny.edu: 1 smu.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 0
  • Total pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: less than a minute
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 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
Pull Request Authors
  • mhahsler (1)
Top Labels
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Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 19,229 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: rRDP

Interface to the RDP Classifier

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 19,229 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 15.4%
Downloads: 46.1%
Maintainers (1)
mhahsler@lyle.smu.edu
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • Biostrings >= 2.26.2 depends
  • rRDPData * suggests