https://github.com/biogenies/tidysq
tidy processing of biological sequences in R
https://github.com/biogenies/tidysq
bioconductor bioinformatics biological-sequences fasta r rstats s3 sequences tibble tidy tidyverse vctrs
Last synced: 10 months ago
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tidy processing of biological sequences in R
- Host: GitHub
- URL: https://github.com/biogenies/tidysq
- Owner: BioGenies
- Created: 2019-07-03T14:01:19.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2025-01-08T18:53:55.000Z (over 1 year ago)
- Last Synced: 2025-04-04T12:53:43.420Z (about 1 year ago)
- Topics: bioconductor, bioinformatics, biological-sequences, fasta, r, rstats, s3, sequences, tibble, tidy, tidyverse, vctrs
- Language: C++
- Homepage: https://BioGenies.github.io/tidysq/
- Size: 10.9 MB
- Stars: 41
- Watchers: 4
- Forks: 4
- Open Issues: 52
-
Metadata Files:
- Readme: README.Rmd
- Changelog: NEWS.md
Awesome Lists containing this project
README
---
output: github_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(
echo = TRUE,
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# tidysq 
[](https://cran.r-project.org/package=tidysq)
[](https://github.com/BioGenies/tidysq/actions)
[](https://lifecycle.r-lib.org/articles/stages.html#experimental)
## Overview
`tidysq` contains tools for analysis and manipulation of biological sequences (including amino acid and nucleic acid -- e.g. RNA, DNA -- sequences). Two major features of this package are:
- effective compression of sequence data, allowing to fit larger datasets in **R**,
- compatibility with most of `tidyverse` universe, especially `dplyr` and `vctrs` packages, making analyses *tidier*.
## Getting started
[Try our quick start vignette](http://biogenies.info/tidysq/articles/quick-start.html) or [our exhaustive documentation](http://biogenies.info/tidysq/reference/index.html).
## Installation
The easiest way to install `tidysq` package is to download its latest version from CRAN repository:
```{r, eval=FALSE}
install.packages("tidysq")
```
Alternatively, it is possible to download the development version directly from GitHub repository:
```{r, eval=FALSE}
# install.packages("devtools")
devtools::install_github("BioGenies/tidysq")
```
## Example usage
```{r, message=FALSE}
library(tidysq)
```
```{r}
file <- system.file("examples", "example_aa.fasta", package = "tidysq")
sqibble <- read_fasta(file)
sqibble
sq_ami <- sqibble$sq
sq_ami
# Subsequences can be extracted with bite()
bite(sq_ami, 5:10)
# There are also more traditional functions
reverse(sq_ami)
# find_motifs() returns a whole tibble of useful informations
find_motifs(sqibble, "^VHX")
```
An example of `dplyr` integration:
```{r, message=FALSE}
library(dplyr)
# tidysq integrates well with dplyr verbs
sqibble %>%
filter(sq %has% "VFF") %>%
mutate(length = get_sq_lengths(sq))
```
## Citation
For citation type:
```{r, eval=FALSE}
citation("tidysq")
```
or use:
Michal Burdukiewicz, Dominik Rafacz, Laura Bakala, Jadwiga Slowik, Weronika Puchala, Filip Pietluch, Katarzyna Sidorczuk, Stefan Roediger and Leon Eyrich Jessen (2021). tidysq: Tidy Processing and Analysis of Biological Sequences. R package version 1.1.3.