{"id":18733533,"url":"https://github.com/insightsengineering/hermes","last_synced_at":"2025-04-12T18:31:49.912Z","repository":{"id":38311464,"uuid":"383270687","full_name":"insightsengineering/hermes","owner":"insightsengineering","description":"Preprocessing, analyzing, and reporting of RNA-seq data","archived":false,"fork":false,"pushed_at":"2025-01-24T15:15:21.000Z","size":55863,"stargazers_count":11,"open_issues_count":2,"forks_count":2,"subscribers_count":21,"default_branch":"main","last_synced_at":"2025-03-22T17:41:58.018Z","etag":null,"topics":["r","r-package","rna-seq","rstats","statistical-engineering"],"latest_commit_sha":null,"homepage":"https://insightsengineering.github.io/hermes/","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/insightsengineering.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":".github/CONTRIBUTING.md","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},"funding":{"custom":["https://pharmaverse.org"]}},"created_at":"2021-07-05T21:42:48.000Z","updated_at":"2025-01-24T15:00:32.000Z","dependencies_parsed_at":"2024-02-13T12:42:26.808Z","dependency_job_id":"66d805cc-1c02-4581-8d82-fc98894c6740","html_url":"https://github.com/insightsengineering/hermes","commit_stats":{"total_commits":562,"total_committers":42,"mean_commits":"13.380952380952381","dds":0.699288256227758,"last_synced_commit":"dc66117fb5d577d72a318e007d83b76927a40f0c"},"previous_names":[],"tags_count":13,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/insightsengineering%2Fhermes","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/insightsengineering%2Fhermes/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/insightsengineering%2Fhermes/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/insightsengineering%2Fhermes/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/insightsengineering","download_url":"https://codeload.github.com/insightsengineering/hermes/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248613544,"owners_count":21133531,"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":["r","r-package","rna-seq","rstats","statistical-engineering"],"created_at":"2024-11-07T15:10:19.639Z","updated_at":"2025-04-12T18:31:48.255Z","avatar_url":"https://github.com/insightsengineering.png","language":"R","funding_links":["https://pharmaverse.org"],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\u003c!-- markdownlint-disable-file --\u003e\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n# hermes \u003cp align=\"center\"\u003e \u003cimg src='man/figures/logo.png' align=\"right\" height=\"131.5\" alt=\"hermes-logo\"/\u003e \u003c/p\u003e\n\n```{r, echo = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"README-\"\n)\n```\n\n\u003c!-- start badges --\u003e\n[![Check 🛠](https://github.com/insightsengineering/hermes/actions/workflows/check.yaml/badge.svg)](https://github.com/insightsengineering/hermes/actions/workflows/check.yaml)\n[![Docs 📚](https://github.com/insightsengineering/hermes/actions/workflows/docs.yaml/badge.svg)](https://insightsengineering.github.io/hermes/)\n[![Code Coverage 📔](https://raw.githubusercontent.com/insightsengineering/hermes/_xml_coverage_reports/data/main/badge.svg)](https://raw.githubusercontent.com/insightsengineering/hermes/_xml_coverage_reports/data/main/coverage.xml)\n\n![GitHub forks](https://img.shields.io/github/forks/insightsengineering/hermes?style=social)\n![GitHub repo stars](https://img.shields.io/github/stars/insightsengineering/hermes?style=social)\n\n![GitHub commit activity](https://img.shields.io/github/commit-activity/m/insightsengineering/hermes)\n![GitHub contributors](https://img.shields.io/github/contributors/insightsengineering/hermes)\n![GitHub last commit](https://img.shields.io/github/last-commit/insightsengineering/hermes)\n![GitHub pull requests](https://img.shields.io/github/issues-pr/insightsengineering/hermes)\n![GitHub repo size](https://img.shields.io/github/repo-size/insightsengineering/hermes)\n![GitHub language count](https://img.shields.io/github/languages/count/insightsengineering/hermes)\n[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)\n[![Current Version](https://img.shields.io/github/r-package/v/insightsengineering/hermes/main?color=purple\\\u0026label=package%20version)](https://github.com/insightsengineering/hermes/tree/main)\n[![Open Issues](https://img.shields.io/github/issues-raw/insightsengineering/hermes?color=red\\\u0026label=open%20issues)](https://github.com/insightsengineering/hermes/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc)\n\u003c!-- end badges --\u003e\n\\\n\n\u003e `hermes` facilitates preprocessing, analyzing, and reporting of RNA-seq data.\n\n- Imports `RNAseq` count data into the `hermes` ready format.\n- Annotates gene information automatically from a central database (e.g. `BioMart`).\n- Adds quality control (QC) flags to genes and samples.\n- Filters the data set.\n- Normalizes the counts.\n- Quickly produces descriptive plots.\n- Performs principal components analysis.\n- Produces a templated QC report.\n- Performs differential expression analysis.\n\n## Installation\n\n### `BioConductor`\n\nYou can install the current release from `BioConductor` with:\n\n```{r bioc-installation, eval = FALSE}\nif (!require(\"BiocManager\")) {\n  install.packages(\"BiocManager\")\n}\nBiocManager::install(\"hermes\")\n```\n\n### GitHub\n\nYou can install the development version from GitHub with:\n\n```{r gh-installation, eval = FALSE}\nif (!require(\"devtools\")) {\n  install.packages(\"devtools\")\n}\ndevtools::install_github(\"insightsengineering/hermes\")\n```\n\n## Getting Started\n\nYou can get started by reading the introduction vignette:\n\n```{r vignette-start, eval = FALSE}\nlibrary(hermes)\nvignette(\"introduction\", package = \"hermes\")\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Finsightsengineering%2Fhermes","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Finsightsengineering%2Fhermes","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Finsightsengineering%2Fhermes/lists"}