{"id":50445480,"url":"https://github.com/sebastian-gregoricchio/rseb","last_synced_at":"2026-05-31T21:02:56.746Z","repository":{"id":44889788,"uuid":"321398522","full_name":"sebastian-gregoricchio/Rseb","owner":"sebastian-gregoricchio","description":"An R-package for daily tasks required to handle biological data as well as avoid re-coding of small functions for quick but necessary data management.","archived":false,"fork":false,"pushed_at":"2026-01-26T12:39:20.000Z","size":11009,"stargazers_count":0,"open_issues_count":1,"forks_count":1,"subscribers_count":1,"default_branch":"main","last_synced_at":"2026-04-19T02:40:06.562Z","etag":null,"topics":["atac-seq","bedtools","chip-seq","cutandtag","daily-tasks","data-visualisation","data-visualization","datamining","deeptools","genomics","ngs","qpcr","qpcr-analysis","r","rna-seq","statistics"],"latest_commit_sha":null,"homepage":"https://sebastian-gregoricchio.github.io/Rseb/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/sebastian-gregoricchio.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"citation.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2020-12-14T15:56:44.000Z","updated_at":"2026-01-26T12:39:24.000Z","dependencies_parsed_at":"2023-02-09T19:15:59.670Z","dependency_job_id":"9e7ae582-0805-462a-a825-253a3f6fafbb","html_url":"https://github.com/sebastian-gregoricchio/Rseb","commit_stats":null,"previous_names":[],"tags_count":14,"template":false,"template_full_name":null,"purl":"pkg:github/sebastian-gregoricchio/Rseb","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sebastian-gregoricchio%2FRseb","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sebastian-gregoricchio%2FRseb/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sebastian-gregoricchio%2FRseb/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sebastian-gregoricchio%2FRseb/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sebastian-gregoricchio","download_url":"https://codeload.github.com/sebastian-gregoricchio/Rseb/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sebastian-gregoricchio%2FRseb/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":33748607,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-05-31T02:00:06.040Z","response_time":95,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":["atac-seq","bedtools","chip-seq","cutandtag","daily-tasks","data-visualisation","data-visualization","datamining","deeptools","genomics","ngs","qpcr","qpcr-analysis","r","rna-seq","statistics"],"created_at":"2026-05-31T21:02:53.850Z","updated_at":"2026-05-31T21:02:56.740Z","avatar_url":"https://github.com/sebastian-gregoricchio.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"![release](https://img.shields.io/github/v/release/sebastian-gregoricchio/Rseb)\r\n[![license](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://sebastian-gregoricchio.github.io/Rseb/LICENSE.md/LICENSE)\r\n[![DOI](https://zenodo.org/badge/321398522.svg)](https://zenodo.org/doi/10.5281/zenodo.13645872)\r\n[![forks](https://img.shields.io/github/forks/sebastian-gregoricchio/Rseb?style=social)](https://github.com/sebastian-gregoricchio/Rseb/fork)\r\n\u003c!-- ![update](https://badges.pufler.dev/updated/sebastian-gregoricchio/Rseb)\r\n![visits](https://badges.pufler.dev/visits/sebastian-gregoricchio/Rseb) --\u003e\r\n\u003c!---![downloads](https://img.shields.io/github/downloads/sebastian-gregoricchio/Rseb/total.svg)---\u003e\r\n\r\n# Rseb [\u003cimg src=\"https://sebastian-gregoricchio.github.io/Rseb/Rseb_logo.svg\" align=\"right\" height = 150/\u003e](https://sebastian-gregoricchio.github.io/Rseb)\r\n\r\nAn R-package for daily tasks required to handle biological data as well as avoid re-coding of small functions for quick but necessary data managing.\r\n\r\n\r\n## Introduction\r\nThe concept behind the `Rseb` (*R*-package for *S*implified *E*nd-to-end data *B*uild-up) is to provide a toolkit that allows the automation of different type of tasks avoiding retyping of code and loss of time. Furthermore, the advantage is that, in most of the cases, the functions are built in R-language making it suitable for all the operating systems\r\n\r\nFrom a more biological point of view, this package simplifies many downstream analyses of high-throughput data that otherwise would require many hours of code typing and case-to-case adaptation. Moreover, most of the functions aimed to visualize these kind of data are thought to provide a high level of possible customization with a large number of graphical parameters compared to the commonly used already available tools. Another advantage of this package is that it offers multiple methods, with a corresponding visualization, to quantify the difference of signal between samples, in a qualitatively and/or quantitatively way, without any additional coding.\r\n\r\nThe guide is divided in three parts: the first one will explore some analyses and visualization of RNA-seq data, the second one the representation and quantification of targeted sequencing data (ChIP-seq, ATAC-seq, etc.), while the last part is focused on some of the \"general\" tools available.\r\n\r\n\r\n\r\n### Citation\r\nIf you use this package, please cite:\r\n\r\n\u003cdiv class=\"warning\" style='padding:2.5%; background-color:#ffffee; color:#787878; margin-left:5%; margin-right:5%; border-radius:15px;'\u003e\r\n\u003cspan\u003e\r\n\u003cfont size=\"-0.5\"\u003e\r\n\r\n\u003cdiv style=\"margin-left:2%; margin-right:2%; text-align: justify\"\u003e\r\n\"HDAC1 and PRC2 mediate combinatorial control in SPI1/PU.1-dependent gene repression in murine erythroleukaemia.\"\r\n\r\nGregoricchio S. *et al.*, *Nucleic Acids Research* (2022)\r\n\r\n*doi*: [10.1093/nar/gkac613](https://doi.org/10.1093/nar/gkac613)\r\n\u003c/div\u003e\r\n\u003c/font\u003e\r\n\r\n\u003c/span\u003e\r\n\u003c/div\u003e\r\n\r\n\r\n\u003cbr\u003e\r\n\r\n\r\n## Dependencies/Requirements\r\n### Unavailble libraries\r\nSome functions require packages that are noy available anymore on Bioconductor (namely `SUSHI` and `diffloop`).\r\nThese can be installed (in the following order) as indicated below:\r\n\r\n```r\r\n# Install remotes from CRAN\r\nif (!require(\"remotes\")) install.packages(\"remotes\")\r\n\r\n# Install SUSHI package\r\nremotes::install_github(\"https://github.com/PhanstielLab/Sushi\",\r\n\t\t\t            build_manual = FALSE,\r\n                        build_vignettes = FALSE)\r\n\r\n# Install diffloop package\r\nremotes::install_github(\"https://github.com/aryeelab/diffloop\",\r\n\t\t\t            build_manual = FALSE,\r\n                        build_vignettes = FALSE)\r\n```\r\n\r\n\r\n\r\n\u003cbr /\u003e\r\n\r\n### deepTools\r\nCertain functions of this package require that `deeptools` is installed on your system. For more information see the [deepTools](https://deeptools.readthedocs.io/en/develop/content/installation.html) installation page.\r\n* **Installation via `conda`**: `conda install -c bioconda deeptools`\r\n* **Command line installation using `pip`**: `pip install deeptools`, All python requirements should be automatically installed.\r\n\r\n\r\n\u003cbr /\u003e\r\n\r\n### bedTools\r\nCertain functions of this package require that `bedtools` is installed on your system. For more information see the [bedTools](https://bedtools.readthedocs.io/en/latest/content/installation.html) installation page.\r\n* **Installation via `conda`**: `conda install -c bioconda bedtools`\r\n* **Command line installation**:\r\n    - Fedora/Centos: `yum install BEDTools`\r\n    - Debian/Ubuntu: `apt-get install bedtools`\r\n    - Homebrew (MacOS): `brew tap homebrew/science; brew install bedtools`\r\n    - MacPorts: `port install bedtools`\r\n\r\n\r\n\u003cbr /\u003e\r\n\r\n## Installation of `Rseb`\r\n```r\r\n# Install remotes from CRAN\r\nif (!require(\"remotes\")) install.packages(\"remotes\")\r\n\r\n# Install the Rseb package\r\nremotes::install_github(\"sebastian-gregoricchio/Rseb\",\r\n\t\t\t            build_manual = TRUE,\r\n                        build_vignettes = TRUE)\r\n```\r\n\u003cbr /\u003e\r\n\r\n## Documentation\r\nWith the package a [PDF manual](https://sebastian-gregoricchio.github.io/Rseb/Rseb_manual.pdf) and a [vignette](https://sebastian-gregoricchio.github.io/Rseb/doc/Rseb.overview.vignette.html) are available.\r\nThe vignette can be inspected on R as well by typing `browseVignettes(\"Rseb\")`.\r\n\r\n\r\n\u003cbr /\u003e\r\n\r\n## Package history and releases\r\nA list of all releases and respective description of changes applied could be found [here](https://sebastian-gregoricchio.github.io/Rseb/NEWS).\r\n\r\n\u003cbr /\u003e\r\n\r\n-----------------\r\n## Contact\r\nFor any suggestion, bug fixing, commentary please report it in the [issues](https://github.com/sebastian-gregoricchio/Rseb/issues)/[request](https://github.com/sebastian-gregoricchio/Rseb/pulls) tab of this repository.\r\n\r\n## License\r\nThis package is under a [GNU General Public License (version 3)](https://sebastian-gregoricchio.github.io/Rseb/LICENSE.md/LICENSE).\r\n\r\n\u003cbr /\u003e\r\n\r\n#### Contributors\r\n[![contributors](https://contrib.rocks/image?repo=sebastian-gregoricchio/Rseb)](https://sebastian-gregoricchio.github.io/)\r\n\r\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsebastian-gregoricchio%2Frseb","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsebastian-gregoricchio%2Frseb","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsebastian-gregoricchio%2Frseb/lists"}