{"id":21023865,"url":"https://github.com/biogenies/tidysq","last_synced_at":"2025-08-18T21:06:24.336Z","repository":{"id":41955456,"uuid":"195065316","full_name":"BioGenies/tidysq","owner":"BioGenies","description":"tidy processing of biological sequences in R","archived":false,"fork":false,"pushed_at":"2025-01-08T18:53:55.000Z","size":11392,"stargazers_count":41,"open_issues_count":52,"forks_count":4,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-04-04T12:53:43.420Z","etag":null,"topics":["bioconductor","bioinformatics","biological-sequences","fasta","r","rstats","s3","sequences","tibble","tidy","tidyverse","vctrs"],"latest_commit_sha":null,"homepage":"https://BioGenies.github.io/tidysq/","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/BioGenies.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-07-03T14:01:19.000Z","updated_at":"2025-03-08T19:29:24.000Z","dependencies_parsed_at":"2024-10-30T22:32:21.943Z","dependency_job_id":"d9980b8e-deb5-4889-8b34-e3812faa4153","html_url":"https://github.com/BioGenies/tidysq","commit_stats":{"total_commits":1324,"total_committers":14,"mean_commits":94.57142857142857,"dds":0.5460725075528701,"last_synced_commit":"51103fe76d2de1a3d947c2ea08c1c98ef72a5f7a"},"previous_names":[],"tags_count":6,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioGenies%2Ftidysq","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioGenies%2Ftidysq/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioGenies%2Ftidysq/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BioGenies%2Ftidysq/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BioGenies","download_url":"https://codeload.github.com/BioGenies/tidysq/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247657276,"owners_count":20974344,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioconductor","bioinformatics","biological-sequences","fasta","r","rstats","s3","sequences","tibble","tidy","tidyverse","vctrs"],"created_at":"2024-11-19T11:20:30.934Z","updated_at":"2025-04-07T13:05:54.270Z","avatar_url":"https://github.com/BioGenies.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n```{r setup, include=FALSE}\nknitr::opts_chunk$set(\n  echo = TRUE,\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  out.width = \"100%\"\n)\n```\n\n# tidysq \u003ca href='https://biogenies.info/tidysq/'\u003e\u003cimg src='man/figures/logo.png' align=\"right\" height=\"139\" /\u003e\u003c/a\u003e\n\n\u003c!-- badges: start --\u003e\n[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/tidysq)](https://cran.r-project.org/package=tidysq)\n  [![Github Actions Build Status](https://github.com/BioGenies/tidysq/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/BioGenies/tidysq/actions)\n  [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)\n\u003c!-- badges: end --\u003e\n\n## Overview\n\n`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:\n\n- effective compression of sequence data, allowing to fit larger datasets in **R**,\n\n- compatibility with most of `tidyverse` universe, especially `dplyr` and `vctrs` packages, making analyses *tidier*.\n\n## Getting started\n\n[Try our quick start vignette](http://biogenies.info/tidysq/articles/quick-start.html) or [our exhaustive documentation](http://biogenies.info/tidysq/reference/index.html).\n\n## Installation\n\nThe easiest way to install `tidysq` package is to download its latest version from CRAN repository:\n\n```{r, eval=FALSE}\ninstall.packages(\"tidysq\")\n```\n\nAlternatively, it is possible to download the development version directly from GitHub repository:\n\n```{r, eval=FALSE}\n# install.packages(\"devtools\")\ndevtools::install_github(\"BioGenies/tidysq\")\n```\n\n## Example usage\n\n```{r, message=FALSE}\nlibrary(tidysq)\n```\n\n```{r}\nfile \u003c- system.file(\"examples\", \"example_aa.fasta\", package = \"tidysq\")\nsqibble \u003c- read_fasta(file)\nsqibble\n\nsq_ami \u003c- sqibble$sq\nsq_ami\n\n# Subsequences can be extracted with bite()\nbite(sq_ami, 5:10)\n\n# There are also more traditional functions\nreverse(sq_ami)\n\n# find_motifs() returns a whole tibble of useful informations\nfind_motifs(sqibble, \"^VHX\")\n```\n\nAn example of `dplyr` integration:\n\n```{r, message=FALSE}\nlibrary(dplyr)\n# tidysq integrates well with dplyr verbs\nsqibble %\u003e%\n  filter(sq %has% \"VFF\") %\u003e%\n  mutate(length = get_sq_lengths(sq))\n```\n\n## Citation\n\nFor citation type:\n\n```{r, eval=FALSE}\ncitation(\"tidysq\")\n```\n\nor use:\n\nMichal 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.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiogenies%2Ftidysq","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiogenies%2Ftidysq","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiogenies%2Ftidysq/lists"}