{"id":13683900,"url":"https://github.com/arc85/celltalker","last_synced_at":"2025-04-30T20:31:43.820Z","repository":{"id":40481438,"uuid":"204349823","full_name":"arc85/celltalker","owner":"arc85","description":"Inference of cell-cell communication from single-cell RNAseq data","archived":true,"fork":false,"pushed_at":"2025-04-21T20:25:16.000Z","size":11639,"stargazers_count":48,"open_issues_count":0,"forks_count":20,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-04-21T21:29:44.515Z","etag":null,"topics":["ligands","receptors","single-cell","transcriptomics"],"latest_commit_sha":null,"homepage":"https://arc85.github.io/celltalker/","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/arc85.png","metadata":{"files":{"readme":"README.Rmd","changelog":null,"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}},"created_at":"2019-08-25T21:06:20.000Z","updated_at":"2025-04-21T20:25:40.000Z","dependencies_parsed_at":"2023-01-19T07:30:35.527Z","dependency_job_id":"0ed27a24-ec75-4f20-b117-5f6b2cb8cb12","html_url":"https://github.com/arc85/celltalker","commit_stats":null,"previous_names":[],"tags_count":5,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/arc85%2Fcelltalker","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/arc85%2Fcelltalker/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/arc85%2Fcelltalker/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/arc85%2Fcelltalker/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/arc85","download_url":"https://codeload.github.com/arc85/celltalker/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":251777555,"owners_count":21642184,"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":["ligands","receptors","single-cell","transcriptomics"],"created_at":"2024-08-02T14:00:20.146Z","updated_at":"2025-04-30T20:31:43.814Z","avatar_url":"https://github.com/arc85.png","language":"R","funding_links":[],"categories":["Uncategorized"],"sub_categories":["Uncategorized"],"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# ARCHIVE NOTICE\n\nThis celltalker repository is archived and no longer maintained. Please check up the celltalker repository at CilloLaboratory/celltalker for the maintained version. \n\n# celltalker\n\nThe goal of celltalker is to infer putative ligand and receptor interactions from single-cell RNAseq data. This is accomplished by evaluating known cognate ligand/receptor interactions across groups of cells. Interactions are scored by jointly weighting the expression levels of ligands and receptors, and significance is evaluated by comparing to a background distribution of scrambled ligands and receptors.\n\nA recent refactoring of this package has made the interface much simpler to use. We also provide a wrapper to the functionality of the [circlize package](https://jokergoo.github.io/circlize_book/book/) for creating circos plots of ligands and receptors.\n\n## Installation\n\nYou can install the development version from [GitHub](https://github.com/) with:\n\n``` r\n# install.packages(\"devtools\")\ndevtools::install_github(\"arc85/celltalker\")\n```\n\n## TL;DR example use\n\nHere's a basic use case for celltalker based on a subset of the 40,000 bone marrow single-cell dataset available from the Human Cell Atlas. Check out SeuratData [here](https://github.com/satijalab/seurat-data) to download the example dataset.\n\nNote that we have identified canonical immune cell types and filtered the dataset for ease of analysis. A vignette documenting this processing is coming soon, but please utilize the **hca_bm_umap_cell_types** data.frame for the vignette below.\n\n```{r example}\n# Load packages\nsuppressMessages({\n  library(celltalker)\n  library(Seurat)\n  suppressWarnings(\n    library(SeuratData)\n  )\n  library(tidyverse)\n})\n\n# Load Human Cell Atlast Bone Marrow from SeuratData\ndata(hcabm40k)\n\n# Filter cell and assign cell types to the dataset\n# NB: hca_bm_umap_cell_types has cell types and UMAP embeddings\nhca_bm \u003c- hcabm40k[,rownames(hca_bm_umap_cell_types)]\nhca_bm[[\"cell_types\"]] \u003c- hca_bm_umap_cell_types$cell_types\n\n# Process data\nhca_bm \u003c- NormalizeData(hca_bm)\n\n# Add UMAP coordinates\nhca_bm[[\"umap\"]] \u003c- CreateDimReducObject(embeddings=as.matrix(hca_bm_umap_cell_types[,1:2]),\n  key=\"UMAP_\",assay=\"RNA\")\n\n# View cell types\nDimPlot(hca_bm,group.by=\"cell_types\")\n\n## Run celltalker\nhca_bm_interactions \u003c- celltalk(input_object=hca_bm,\n  metadata_grouping=\"cell_types\",\n  ligand_receptor_pairs=ramilowski_pairs,\n  number_cells_required=100,\n  min_expression=1000,\n  max_expression=20000,\n  scramble_times=10)\n\n## Identify top statistically significant interactions\ntop_stats \u003c- hca_bm_interactions %\u003e%\n  mutate(fdr=p.adjust(p_val,method=\"fdr\")) %\u003e%\n  filter(fdr\u003c0.05) %\u003e%\n  group_by(cell_type1) %\u003e%\n  top_n(3,interact_ratio) %\u003e%\n  ungroup()\n\n## Generate a circos plot\ncolors_use \u003c- RColorBrewer::brewer.pal(n=length(unique(hca_bm$cell_types)),\"Set2\")\n\ncircos_plot(ligand_receptor_frame=top_stats,\n  cell_group_colors=colors_use,\n  ligand_color=\"blue\",\n  receptor_color=\"red\",\n  cex_outer=0.5,\n  cex_inner=0.4)\n\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Farc85%2Fcelltalker","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Farc85%2Fcelltalker","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Farc85%2Fcelltalker/lists"}