{"id":16319337,"url":"https://github.com/lcolladotor/derfinder","last_synced_at":"2025-04-13T05:36:05.721Z","repository":{"id":9588537,"uuid":"11506480","full_name":"lcolladotor/derfinder","owner":"lcolladotor","description":"Annotation-agnostic differential expression analysis of RNA-seq data via expressed regions-level or single base-level approaches","archived":false,"fork":false,"pushed_at":"2024-05-03T13:34:18.000Z","size":12019,"stargazers_count":42,"open_issues_count":3,"forks_count":15,"subscribers_count":24,"default_branch":"devel","last_synced_at":"2024-10-11T22:26:36.146Z","etag":null,"topics":["annotation-agnostic","bioconductor","derfinder","r","rnaseq","rstats"],"latest_commit_sha":null,"homepage":"http://lcolladotor.github.io/derfinder","language":"R","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/lcolladotor.png","metadata":{"files":{"readme":"README.Rmd","changelog":null,"contributing":".github/CONTRIBUTING.md","funding":null,"license":null,"code_of_conduct":".github/CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":".github/SUPPORT.md","governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2013-07-18T15:31:22.000Z","updated_at":"2024-05-03T13:34:23.000Z","dependencies_parsed_at":"2022-07-13T10:00:28.437Z","dependency_job_id":"75851893-e250-4ba0-9d7a-08daf333afd6","html_url":"https://github.com/lcolladotor/derfinder","commit_stats":{"total_commits":888,"total_committers":22,"mean_commits":40.36363636363637,"dds":"0.36599099099099097","last_synced_commit":"f9cd986e0c1b9ea6551d0d8d2077d4501216a661"},"previous_names":[],"tags_count":17,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lcolladotor%2Fderfinder","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lcolladotor%2Fderfinder/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lcolladotor%2Fderfinder/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lcolladotor%2Fderfinder/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lcolladotor","download_url":"https://codeload.github.com/lcolladotor/derfinder/tar.gz/refs/heads/devel","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248670507,"owners_count":21142897,"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":["annotation-agnostic","bioconductor","derfinder","r","rnaseq","rstats"],"created_at":"2024-10-10T22:26:37.319Z","updated_at":"2025-04-13T05:36:05.696Z","avatar_url":"https://github.com/lcolladotor.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n    collapse = TRUE,\n    comment = \"#\u003e\",\n    fig.path = \"man/figures/README-\",\n    out.width = \"100%\"\n)\n```\n\n# derfinder\n\n\u003c!-- badges: start --\u003e\n[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)\n[![Bioc release status](http://www.bioconductor.org/shields/build/release/bioc/derfinder.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/derfinder)\n[![Bioc devel status](http://www.bioconductor.org/shields/build/devel/bioc/derfinder.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/derfinder)\n[![Bioc downloads rank](https://bioconductor.org/shields/downloads/release/derfinder.svg)](http://bioconductor.org/packages/stats/bioc/derfinder/)\n[![Bioc support](https://bioconductor.org/shields/posts/derfinder.svg)](https://support.bioconductor.org/tag/derfinder)\n[![Bioc history](https://bioconductor.org/shields/years-in-bioc/derfinder.svg)](https://bioconductor.org/packages/release/bioc/html/derfinder.html#since)\n[![Bioc last commit](https://bioconductor.org/shields/lastcommit/devel/bioc/derfinder.svg)](http://bioconductor.org/checkResults/devel/bioc-LATEST/derfinder/)\n[![Bioc dependencies](https://bioconductor.org/shields/dependencies/release/derfinder.svg)](https://bioconductor.org/packages/release/bioc/html/derfinder.html#since)\n[![Codecov test coverage](https://codecov.io/gh/lcolladotor/derfinder/branch/devel/graph/badge.svg)](https://codecov.io/gh/lcolladotor/derfinder?branch=devel)\n[![R build status](https://github.com/lcolladotor/derfinder/actions/workflows/check-bioc.yml/badge.svg)](https://github.com/lcolladotor/derfinder/actions/workflows/check-bioc.yml)\n[![GitHub issues](https://img.shields.io/github/issues/lcolladotor/derfinder)](https://github.com/lcolladotor/derfinder/issues)\n[![GitHub pulls](https://img.shields.io/github/issues-pr/lcolladotor/derfinder)](https://github.com/lcolladotor/derfinder/pulls)\n\u003c!-- badges: end --\u003e\n\nAnnotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach. This package contains two different implementations of this approach. The first one is the single base-level F-statistics implementation and the second one is via identifying expressed regions. For more information about `derfinder` check the vignettes [here](http://www.bioconductor.org/packages/derfinder).\n\n## Documentation\n\nFor more information about `derfinder` check the vignettes [through Bioconductor](http://bioconductor.org/packages/derfinder) or at the [documentation website](http://lcolladotor.github.io/derfinder).\n\n## Further documentation\n\nYou can generate HTML reports from the results using __regionReport__ \navailable [here](https://github.com/lcolladotor/regionReport).\n\n## Installation instructions\n\nGet the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `derfinder` from [Bioconductor](http://bioconductor.org/) using the following code:\n\n```{r 'install', eval = FALSE}\nif (!requireNamespace(\"BiocManager\", quietly = TRUE)) {\n    install.packages(\"BiocManager\")\n}\n\nBiocManager::install(\"derfinder\")\n```\n\n## Citation\n\nBelow is the citation output from using `citation('derfinder')` in R. Please \nrun this yourself to check for any updates on how to cite __derfinder__.\n\n```{r 'citation', eval = requireNamespace('derfinder')}\nprint(citation(\"derfinder\"), bibtex = TRUE)\n```\n\nPlease note that the `derfinder` was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.\n\n## DER Finder versions\n\n* The original implementation of the DER Finder approach as published in Frazee et al, Biostatistics 2014 is available via GitHub at [derfinder](https://github.com/leekgroup/derfinder).\n* The version implementing the single base-level approach via calculating F-stastics as described in the pre-print Collado-Torres et al, Nucleic Acids Research 2017 is available via Bioconductor at [derfinder](http://bioconductor.org/packages/derfinder). The same package has the functions required for the expressed regions-level approach.\n\n## Code of Conduct\n  \nPlease note that the derfinder project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.\n\n## Development tools\n\n* Continuous code testing is possible thanks to [GitHub actions](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/)  through `r BiocStyle::CRANpkg('usethis')`, `r BiocStyle::CRANpkg('remotes')`, `r BiocStyle::Githubpkg('r-hub/sysreqs')` and `r BiocStyle::CRANpkg('rcmdcheck')` customized to use [Bioconductor's docker containers](https://www.bioconductor.org/help/docker/) and `r BiocStyle::Biocpkg('BiocCheck')`.\n* Code coverage assessment is possible thanks to [codecov](https://codecov.io/gh) and `r BiocStyle::CRANpkg('covr')`.\n* The [documentation website](http://lcolladotor.github.io/derfinder) is automatically updated thanks to `r BiocStyle::CRANpkg('pkgdown')`.\n* The code is styled automatically thanks to `r BiocStyle::CRANpkg('styler')`.\n* The documentation is formatted thanks to `r BiocStyle::CRANpkg('devtools')` and `r BiocStyle::CRANpkg('roxygen2')`.\n\nFor more details, check the `dev` directory.\n\nThis package was developed using `r BiocStyle::Biocpkg('biocthis')`.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flcolladotor%2Fderfinder","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flcolladotor%2Fderfinder","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flcolladotor%2Fderfinder/lists"}