{"id":15629005,"url":"https://github.com/pwwang/hitype","last_synced_at":"2026-05-15T05:33:19.841Z","repository":{"id":188626380,"uuid":"679108100","full_name":"pwwang/hitype","owner":"pwwang","description":"Hierarchical and high-resolution cell-type identification for single-cell RNA-seq data based on ScType.","archived":false,"fork":false,"pushed_at":"2023-10-11T22:37:59.000Z","size":5104,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-02-04T19:13:10.620Z","etag":null,"topics":["cell-type-annotation","cell-type-identification","scrna-seq-analysis","single-cell-rna-seq"],"latest_commit_sha":null,"homepage":"https://pwwang.github.io/hitype/","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/pwwang.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":null,"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}},"created_at":"2023-08-16T05:45:02.000Z","updated_at":"2023-08-25T23:52:56.000Z","dependencies_parsed_at":"2023-10-12T05:31:45.095Z","dependency_job_id":null,"html_url":"https://github.com/pwwang/hitype","commit_stats":null,"previous_names":["pwwang/hitype"],"tags_count":4,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pwwang%2Fhitype","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pwwang%2Fhitype/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pwwang%2Fhitype/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pwwang%2Fhitype/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pwwang","download_url":"https://codeload.github.com/pwwang/hitype/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246223323,"owners_count":20743167,"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":["cell-type-annotation","cell-type-identification","scrna-seq-analysis","single-cell-rna-seq"],"created_at":"2024-10-03T10:25:18.190Z","updated_at":"2026-05-15T05:33:19.807Z","avatar_url":"https://github.com/pwwang.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# hitype \u003ca href=\"https://pwwang.github.io/hitype/\"\u003e\u003cimg src=\"man/figures/logo.png\" align=\"right\" height=\"139\" alt=\"hitype website\" /\u003e\u003c/a\u003e\n\n\u003c!-- badges: start --\u003e\n\u003c!-- badges: end --\u003e\n\n**Hi**erarchical and **hi**gh-resolution cell-type identification for single-cell RNA-seq data inspired by [ScType][1].\n\n## Features\n\n- [x] Compatibility with [ScType][1]\n- [x] Hierarchical and high-resolution cell-type identification\n- [x] Train weights for your markers with a reference dataset\n- [x] Speed optimization\n- [x] Support as an R package with unit tests\n\n[1]: https://github.com/IanevskiAleksandr/sc-type\n\n## Installation\n\nYou can install the development version of `hitype` like so:\n\n``` r\nif (!requireNamespace(\"devtools\", quietly = TRUE)) {\n    install.packages(\"devtools\")\n}\ndevtools::install_github(\"pwwang/hitype\")\n```\n\n## Quick start\n\n### Prepare the dataset\n\nSee also \u003chttps://satijalab.org/seurat/articles/pbmc3k_tutorial.html#setup-the-seurat-object\u003e\n\n\u003cdetails\u003e\n  \u003csummary\u003eClick to expand\u003c/summary\u003e\n\n```{r, warning=FALSE, message=FALSE}\npbmc \u003c- pbmc3k.SeuratData::pbmc3k\npbmc[[\"percent.mt\"]] \u003c- Seurat::PercentageFeatureSet(pbmc, pattern = \"^MT-\")\npbmc \u003c- subset(pbmc, subset = nFeature_RNA \u003e 200 \u0026 nFeature_RNA \u003c 2500 \u0026 percent.mt \u003c 5)\npbmc \u003c- Seurat::NormalizeData(pbmc)\npbmc \u003c- Seurat::FindVariableFeatures(pbmc, selection.method = \"vst\", nfeatures = 2000)\npbmc \u003c- Seurat::ScaleData(pbmc, features = rownames(pbmc))\npbmc \u003c- Seurat::RunPCA(pbmc, features = Seurat::VariableFeatures(object = pbmc))\npbmc \u003c- Seurat::FindNeighbors(pbmc, dims = 1:10)\npbmc \u003c- Seurat::FindClusters(pbmc, resolution = 0.5)\npbmc \u003c- Seurat::RunUMAP(pbmc, dims = 1:10)\n```\n\u003c/details\u003e\n\n### Use as a Seurat extension\n\n```{r, warning=FALSE, out.width=\"75%\"}\nlibrary(hitype)\n\n# Load gene sets\ngs \u003c- gs_prepare(hitypedb_pbmc3k)\n\n# Assign cell types\nobj \u003c- RunHitype(pbmc, gs)\n\nSeurat::DimPlot(obj, group.by = \"hitype\", label = TRUE, label.box = TRUE) +\n  Seurat::NoLegend()\n```\n\nCompared to the manual marked cell types:\n![Seurat manual marked cell types](https://satijalab.org/seurat/articles/pbmc3k_tutorial_files/figure-html/labelplot-1.png){width=75%}\n\nSee also \u003chttps://satijalab.org/seurat/articles/pbmc3k_tutorial.html#assigning-cell-type-identity-to-clusters\u003e\n\n### Use as standalone functions\n\n```{r, warning=FALSE}\nscores \u003c- hitype_score(pbmc@assays$RNA@scale.data, gs, scaled = TRUE)\ncell_types \u003c- hitype_assign(pbmc$seurat_clusters, scores, gs)\nsummary(cell_types)\n```\n\nYou may see that we have exactly the same assignment in the Seurat tutorial:\n\n|Cluster ID\t| Markers | Cell Type |\n|:----------|:--------|:----------|\n|0|\tIL7R, CCR7 |\tNaive CD4+ T |\n|1|\tCD14, LYZ |\tCD14+ Mono|\n|2|\tIL7R, S100A4 | Memory CD4+|\n|3|\tMS4A1 | B|\n|4|\tCD8A | CD8+ T|\n|5|\tFCGR3A, MS4A7 | FCGR3A+ Mono|\n|6|\tGNLY, NKG7 | NK|\n|7|\tFCER1A, CST3 | DC|\n|8|\tPPBP | Platelet|\n\n## Documentation\n\n\u003chttps://pwwang.github.io/hitype/\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpwwang%2Fhitype","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpwwang%2Fhitype","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpwwang%2Fhitype/lists"}