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rBLAST

Interface for the Basic Local Alignment Search Tool (BLAST) - R-Package

https://github.com/mhahsler/rblast

Science Score: 36.0%

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
  • ✓
    Academic publication links
    Links to: ncbi.nlm.nih.gov
  • ○
    Committers with academic emails
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    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.1%) to scientific vocabulary

Keywords

bioconductor bioinformatics blast-search
Last synced: 6 months ago · JSON representation

Repository

Interface for the Basic Local Alignment Search Tool (BLAST) - R-Package

Basic Info
  • Host: GitHub
  • Owner: mhahsler
  • License: gpl-3.0
  • Language: R
  • Default Branch: devel
  • Homepage:
  • Size: 457 KB
Statistics
  • Stars: 111
  • Watchers: 3
  • Forks: 22
  • Open Issues: 3
  • Releases: 0
Topics
bioconductor bioinformatics blast-search
Created over 10 years ago · Last pushed 8 months ago
Metadata Files
Readme Changelog License

README.Rmd 

---
output: github_document
---



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

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

Interfaces the Basic Local Alignment Search Tool (BLAST) to search genetic sequence data bases with the Bioconductor infrastructure. This includes
interfaces to `blastn`, `blastp`, `blastx`, and `makeblastdb`.
The BLAST software needs to be downloaded and installed separately.

Other R interfaces for bioinformatics are also available:

* [rRDP](https://bioconductor.org/packages/rRDP): Interface to the RDP Classifier 
* [rMSA](https://mhahsler.r-universe.dev/rMSA): Interface for Popular Multiple 
    Sequence Alignment Tools including ClustalW, MAFFT, MUSCLE, and Kalign


## Installation

1. Install the BLAST software by following the instructions in the 
[INSTALL](https://github.com/mhahsler/rBLAST/blob/devel/INSTALL) file.

2. Install the latest version of the R package
    ```{r eval = FALSE}
    if (!require("BiocManager", quietly = TRUE)) {
        install.packages("BiocManager")
    }
    
    # The following initializes usage of Bioc devel
    BiocManager::install(version='devel')
    
    BiocManager::install("rBLAST")
    ```

## Usage

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

Download the prebuilt 16S Microbial data base from NCBI's ftp server at:
https://ftp.ncbi.nlm.nih.gov/blast/db/

```{r}
tgz_file <- blast_db_get("16S_ribosomal_RNA.tar.gz")
untar(tgz_file, exdir = "16S_rRNA_DB")
```

Load the downloaded BLAST database.
```{r}
bl <- blast(db = "./16S_rRNA_DB/16S_ribosomal_RNA")
bl
```

Load some test sequences shipped with the package.

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

Query the BLAST database to find matches for the first test sequence
with a 99% percent identity or higher.

```{r}
cl <- predict(bl, seq[1, ], BLAST_args = "-perc_identity 99")
cl
```

```{r, include=FALSE}
unlink("./16S_rRNA_DB", recursive = TRUE)
```

## 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
  • Issues event: 7
  • Watch event: 7
  • Issue comment event: 8
  • Push event: 3
Last Year
  • Issues event: 7
  • Watch event: 7
  • Issue comment event: 8
  • Push event: 3

Committers

Last synced: 10 months ago

All Time
  • Total Commits: 60
  • Total Committers: 4
  • Avg Commits per committer: 15.0
  • Development Distribution Score (DDS): 0.1
Past Year
  • Commits: 3
  • Committers: 2
  • Avg Commits per committer: 1.5
  • Development Distribution Score (DDS): 0.333
Top Committers
Name Email Commits
Michael Hahsler m****l@h****t 54
J Wokaty j****y 4
Thomas Shafee T****4 1
Jan-Philipp Quast 5****t 1
Committer Domains (Top 20 + Academic)
hahsler.net: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 33
  • Total pull requests: 3
  • Average time to close issues: 10 months
  • Average time to close pull requests: 10 months
  • Total issue authors: 31
  • Total pull request authors: 3
  • Average comments per issue: 3.33
  • Average comments per pull request: 1.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: about 21 hours
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 3.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • kuzmenkov111 (3)
  • uuuuuuuup (1)
  • abrozzi (1)
  • vishalsnegi (1)
  • CamilaDuarte (1)
  • katievigil (1)
  • joaquinhenriquez (1)
  • SilSanGon (1)
  • Ecotone23 (1)
  • hobieslr (1)
  • Sbu211 (1)
  • cgapp13 (1)
  • cjieming2 (1)
  • padpadpadpad (1)
  • amyruthvandiver (1)
Pull Request Authors
  • yzhong005 (2)
  • jpquast (1)
  • TS404 (1)
Top Labels
Issue Labels
enhancement (4) help wanted (3) bug (3) question (1) invalid (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 6,328 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 3
  • Total maintainers: 1
bioconductor.org: rBLAST

R Interface for the Basic Local Alignment Search Tool

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 6,328 Total
Rankings
Dependent repos count: 0.0%
Average: 15.6%
Dependent packages count: 31.3%
Maintainers (1)
mhahsler@lyle.smu.edu
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • Biostrings >= 2.26.2 depends
  • methods * imports