{"id":18501579,"url":"https://github.com/const-ae/highlyreplicatedrnaseq","last_synced_at":"2025-05-14T07:32:08.394Z","repository":{"id":82391848,"uuid":"249515847","full_name":"const-ae/HighlyReplicatedRNASeq","owner":"const-ae","description":"Collection of Bulk RNA-Seq Experiments With Many Replicates","archived":false,"fork":false,"pushed_at":"2021-01-18T12:00:49.000Z","size":36,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-02-17T01:42:18.054Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/const-ae.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":null,"funding":null,"license":"LICENSE","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":"2020-03-23T18:45:29.000Z","updated_at":"2021-01-18T12:00:52.000Z","dependencies_parsed_at":"2023-04-19T23:31:58.604Z","dependency_job_id":null,"html_url":"https://github.com/const-ae/HighlyReplicatedRNASeq","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2FHighlyReplicatedRNASeq","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2FHighlyReplicatedRNASeq/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2FHighlyReplicatedRNASeq/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/const-ae%2FHighlyReplicatedRNASeq/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/const-ae","download_url":"https://codeload.github.com/const-ae/HighlyReplicatedRNASeq/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":254095169,"owners_count":22013720,"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":[],"created_at":"2024-11-06T13:54:20.615Z","updated_at":"2025-05-14T07:32:08.368Z","avatar_url":"https://github.com/const-ae.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# HighlyReplicatedRNASeq\n\n\u003c!-- badges: start --\u003e\n\u003c!-- badges: end --\u003e\n\n\u003e Collection of Bulk RNA-Seq Experiments With Many Replicates\n\nThe HighlyReplicatedRNASeq package provides access to the count matrix results\nfrom studies with many replicates. These datasets can be valuable for\nbenchmarking tools designed to handle RNA-seq data.\n\n## Installation\n\nYou can install the latest version of `r BiocStyle::Biocpkg(\"HighlyReplicatedRNASeq\")` with\n\n``` r\nif (!requireNamespace(\"BiocManager\", quietly = TRUE))\n    install.packages(\"BiocManager\")\n\nBiocManager::install(\"HighlyReplicatedRNASeq\")\n```\n\nTo get the latest development version, install the package from [Github](https://github.com/const-ae/HighlyReplicatedRNASeq)\n\n``` r\n# install.packages(\"devtools\")\ndevtools::install_github(\"const-ae/HighlyReplicatedRNASeq\")\n```\n\n## Datasets\n\n+ Schurch et al. (2016): 86 samples of S. *cerevisiae* in two conditions\n   - `Schurch16()` / `Schurch16_metadata()`\n\n\nAt the moment, this package contains only one dataset, but more datasets can be added in the future.\n\n\n## Example\n\nLoad the `Schurch16` dataset by calling the corresponding function. The first time you run this command, it will download the dataset and will subsequently cache it in a directory that is by `getExperimentHubOption(\"CACHE\")`.\n\n```{r}\nschurch_se \u003c- HighlyReplicatedRNASeq::Schurch16()\nschurch_se\n```\n\n\n## References\n\nSchurch, N. J., Schofield, P., Gierliński, M., Cole, C., Sherstnev, A., Singh, V., … Barton, G. J. (2016). \nHow many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? \\emph{RNA}, 22(6), 839–851. https://doi.org/10.1261/rna.053959.115\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fconst-ae%2Fhighlyreplicatedrnaseq","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fconst-ae%2Fhighlyreplicatedrnaseq","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fconst-ae%2Fhighlyreplicatedrnaseq/lists"}