{"id":32111014,"url":"https://github.com/almeidasilvaf/hybridexpress","last_synced_at":"2026-02-18T20:31:42.488Z","repository":{"id":205154523,"uuid":"706017358","full_name":"almeidasilvaf/HybridExpress","owner":"almeidasilvaf","description":"An R package for comparative transcriptomic analyses of hybrids and their progenitors","archived":false,"fork":false,"pushed_at":"2024-09-05T06:27:48.000Z","size":20091,"stargazers_count":14,"open_issues_count":0,"forks_count":3,"subscribers_count":2,"default_branch":"devel","last_synced_at":"2025-09-28T22:25:08.092Z","etag":null,"topics":["gene-expression","hybrid","polyploidy","rna-seq","transcriptomics"],"latest_commit_sha":null,"homepage":"https://almeidasilvaf.github.io/HybridExpress","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/almeidasilvaf.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":null,"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":"2023-10-17T06:33:02.000Z","updated_at":"2025-03-07T15:43:38.000Z","dependencies_parsed_at":null,"dependency_job_id":"61e6446d-13ab-4f20-a80a-c6f94efe242f","html_url":"https://github.com/almeidasilvaf/HybridExpress","commit_stats":null,"previous_names":["almeidasilvaf/hybridexpress"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/almeidasilvaf/HybridExpress","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/almeidasilvaf%2FHybridExpress","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/almeidasilvaf%2FHybridExpress/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/almeidasilvaf%2FHybridExpress/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/almeidasilvaf%2FHybridExpress/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/almeidasilvaf","download_url":"https://codeload.github.com/almeidasilvaf/HybridExpress/tar.gz/refs/heads/devel","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/almeidasilvaf%2FHybridExpress/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":280103272,"owners_count":26272518,"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","status":"online","status_checked_at":"2025-10-20T02:00:06.978Z","response_time":62,"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":["gene-expression","hybrid","polyploidy","rna-seq","transcriptomics"],"created_at":"2025-10-20T14:10:57.261Z","updated_at":"2025-10-20T14:11:01.830Z","avatar_url":"https://github.com/almeidasilvaf.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# HybridExpress \u003cimg src=\"man/figures/logo.png\" align=\"right\" height=\"139\" alt=\"\" /\u003e\n\n\u003c!-- badges: start --\u003e\n[![GitHub issues](https://img.shields.io/github/issues/almeidasilvaf/HybridExpress)](https://github.com/almeidasilvaf/HybridExpress/issues)\n[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-green.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)\n[![check-bioc](https://github.com/almeidasilvaf/HybridExpress/actions/workflows/rworkflows.devel.yml/badge.svg)](https://github.com/almeidasilvaf/HybridExpress/actions/workflows/rworkflows.devel.yml)\n[![Codecov test coverage](https://codecov.io/gh/almeidasilvaf/HybridExpress/branch/devel/graph/badge.svg)](https://app.codecov.io/gh/almeidasilvaf/HybridExpress?branch=devel)\n\u003c!-- badges: end --\u003e\n\nThe goal of `HybridExpress` is to perform comparative transcriptomic analyses\nof hybrids relative to their progenitor species (a.k.a. *experimental trios*).\nThe package features:\n\n1. **Calculation of midparent expression values**, which are *in silico* \nsamples obtained from the mean, sum, or weighted mean of random sample pairs\nfrom each parent;\n2. **Exploratory analyses of sample grouping** with PCA plots and heatmaps\nof hierarchically-clustered pairwise sample correlations;\n3. **Identification of differentially expressed genes** between hybrids and\ntheir progenitor species, hybrids and midparent values, and the two parents.\nIf spike-in standards are available, `HybridExpress` uses them to normalize\nthe count data by transcriptome size;\n4. **Classification of genes in expression-based categories and classes**\nbased on [Rapp et al. (2009)](https://doi.org/10.1186/1741-7007-7-18). The 12\nexpression categories \nproposed by [Rapp et al. (2009)](https://doi.org/10.1186/1741-7007-7-18) are\ngrouped into 5 major classes (transgressive up-regulation, transgressive\ndown-regulation, additivity, expression-level dominance toward parent 1,\nand expression-level dominance toward parent 2);\n5. **Functional analyses** through the identification of overrepresented\nfunctional terms for gene sets of interest.\n\n\n## Installation instructions\n\nGet the latest stable `R` release from [CRAN](http://cran.r-project.org/). Then install `HybridExpress` 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(\"HybridExpress\")\n```\n\nAnd the development version from [GitHub](https://github.com/almeidasilvaf/HybridExpress) with:\n\n```{r 'install_dev', eval = FALSE}\nBiocManager::install(\"almeidasilvaf/HybridExpress\")\n```\n\n## Citation\n\nBelow is the citation output from using `citation('HybridExpress')` in R. Please\nrun this yourself to check for any updates on how to cite __HybridExpress__.\n\n```{r 'citation', eval = requireNamespace('HybridExpress')}\nprint(citation('HybridExpress'), bibtex = TRUE)\n```\n\nPlease note that the `HybridExpress` 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## Code of Conduct\n\nPlease note that the `HybridExpress` project is released with a [Contributor Code of Conduct](http://bioconductor.org/about/code-of-conduct/). 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')`, 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://almeidasilvaf.github.io/HybridExpress) is automatically updated thanks to `r BiocStyle::CRANpkg('pkgdown')`.\n* The documentation is formatted thanks to `r BiocStyle::CRANpkg('devtools')` and `r BiocStyle::CRANpkg('roxygen2')`.\n\nThis package was developed using `r BiocStyle::Biocpkg('biocthis')`.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falmeidasilvaf%2Fhybridexpress","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Falmeidasilvaf%2Fhybridexpress","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falmeidasilvaf%2Fhybridexpress/lists"}