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alphabetr

R package for obtaining TCR alpha-beta sequence pairs

https://github.com/edwardslee/alphabetr

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
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: plos.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.4%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

R package for obtaining TCR alpha-beta sequence pairs

Basic Info
  • Host: GitHub
  • Owner: edwardslee
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 1 MB
Statistics
  • Stars: 8
  • Watchers: 2
  • Forks: 3
  • Open Issues: 4
  • Releases: 0
Created about 10 years ago · Last pushed over 9 years ago
Metadata Files
Readme

README.Rmd 

---
output:
  md_document:
    variant: markdown_github
---

```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

## alphabetr
`alphabetr` implements the ALPHABETR (algorithm for pairing alpha-beta T cell receptors) algorithms for obtaining TCR sequence pairs. This approach determines CDR3A/CDR3B pairs from high-throughput sequencing data from repeated samples of antigen-specific T cell populations. 

With `alphabetr`, you can

* Determine CDR3A/CDR3B pairs
* Determine dual TCR-alpha clones and clones that share CDR3A or CDR3B sequences
* Estimate clonal frequencies

You can install

* the latest version released on CRAN with
```{r eval = FALSE}
install.packages("alphabetr")
```
* the latest development version found on github with
```{r eval = FALSE}
if (packageVersion("devtools") < 1.6) {
  install.packages("devtools")
}
devtools::install_github("edwardslee/alphabetr")
```

If you encounter any bugs, please file an [issue](https://github.com/edwardslee/alphabetr/issues).

## More information
Please see [our paper in PLOS Computational Biology](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005313) for more details about the algorithm and how it was tested (DOI: 10.1371/journal.pcbi.1005313).

Owner

  • Name: Edward Lee
  • Login: edwardslee
  • Kind: user
  • Location: Glasgow, UK

GitHub Events

Total
Last Year

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 79
  • Total Committers: 1
  • Avg Commits per committer: 79.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Edward Lee e****e@g****m 79

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 4
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 4
  • Total pull request authors: 0
  • Average comments per issue: 1.75
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • 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
  • edwardslee (1)
  • almaan (1)
  • laurajohnson (1)
  • MiryamSpektor (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 226 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 1
  • Total maintainers: 1
cran.r-project.org: alphabetr

Algorithms for High-Throughput Sequencing of Antigen-Specific T Cells

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 226 Last month
Rankings
Forks count: 14.9%
Stargazers count: 18.7%
Average: 28.9%
Dependent packages count: 29.8%
Dependent repos count: 35.5%
Downloads: 45.7%
Maintainers (1)
email.edwardlee@gmail.com
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • Rcpp >= 0.12.3 imports
  • clue >= 0.3 imports
  • dplyr >= 0.4.3 imports
  • multicool >= 0.1 imports
  • knitr * suggests
  • rmarkdown * suggests