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"User_manual_introduction.Rmd", "filename": "User_manual_introduction.html", "title": "Decoding T- and B-cell receptor repertoires with ClustIRR", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "System requirements", "ClustIRR algorithm", "Input", "Algorithm", "Step 1. Compute TCR clonotype similarities in a repertoire with cluster_irr", "Step 2-3. Construct TCR repertoire graphs and join them into $J$", "Run steps 1-3 with clustirr", "Inspect the content of clust_irrs", "Inspect graphs with plot_graph", "You can evaluate $J$ with igraph", "Step 4. community detection with detect_communities", "Inspecting the outputs of detect_communities", "Qualitative similarity between community abundance vectors with get_honeycombs", "Quantitative similarity between community abundance vectors with get_cosine_similarity", "Summary of communities is provided in the detect_communities outputs", "Special functions: decoding communities with decode_community", "Step 5. differential community occupancy (DCO) with dco", "Step 6. Inspect results", "Visualizing the distribution of $\\beta$ with get_beta_violin_ag", "Compare $\\beta$s of clonotypes specific for CMV, EBV, flu or MLANA?", "Posterior predictive checks", "Differential community abundance results $\\rightarrow$ par. $\\delta$", "Conclusion: you can also use custom community occupancy matrix for DCO!" ], "created": "2026-01-05 16:13:08", "modified": "2026-04-10 10:48:11", "commits": 5 }, { "source": "User_manual_groups.Rmd", "filename": "User_manual_groups.html", "title": "Finding biological condition-specific changes in T- and B-cell receptor repertoires with ClustIRR", "engine": "knitr::rmarkdown", "headings": [], "created": "2026-01-05 16:13:08", "modified": "2026-04-09 11:36:01", "commits": 5 } ], "_score": 6.363611979892145, "_indexed": true, "_nocasepkg": "clustirr", "_universes": [ "bioc", "snaketron" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.11.0", "date": "2026-05-30T05:34:12.000Z", "distro": "noble", "arch": "aarch64", "commit": "2fea7dd47b04f2da7c94eccfe80d13485a7a90e6", "fileid": "2de585fdfedad3e82b7ec1b81921a4fe51213d55b59bbb4ddf1bee0778a3d8c9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675555080" }, { "r": "4.7.0", "os": "linux", "version": "1.11.0", "date": "2026-05-30T05:34:54.000Z", "distro": "noble", "arch": "x86_64", "commit": "2fea7dd47b04f2da7c94eccfe80d13485a7a90e6", "fileid": "ad48236d00f7da0cec6e9ada9a6d250ac8bfe7b695b65e0a0011dfac518040e2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675555080" }, { "r": "4.6.0", "os": "linux", "version": "1.11.0", "date": "2026-05-30T05:33:55.000Z", "distro": "noble", "arch": "aarch64", "commit": "2fea7dd47b04f2da7c94eccfe80d13485a7a90e6", "fileid": "68e14b6c96ac10d6ced1ef51e6a1fd14c0d1e0a20b9259ff38823cfdd024c0b4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675555080" }, { "r": "4.6.0", "os": "linux", "version": "1.11.0", "date": "2026-05-30T05:34:05.000Z", "distro": "noble", "arch": "x86_64", "commit": "2fea7dd47b04f2da7c94eccfe80d13485a7a90e6", "fileid": "da2c47bbc0c511d2a8d60b311e23a833234aad70f5570506f70ede3ff159b045", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675555080" }, { "r": "4.5.3", "os": "mac", "version": "1.11.0", "date": "2026-05-30T05:55:40.000Z", "arch": "aarch64", "commit": "2fea7dd47b04f2da7c94eccfe80d13485a7a90e6", "fileid": "ffac0aca227d00e6a66efafe944370fe13a3cf9ad5b8d81a822fec781b3db970", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675555080" }, { "r": "4.5.3", "os": "mac", "version": "1.11.0", "date": "2026-05-30T05:53:57.000Z", "arch": "x86_64", "commit": "2fea7dd47b04f2da7c94eccfe80d13485a7a90e6", "fileid": "0306ef73e2beef482a899562c3b5edea40d5c23c853e6bd5ad32d83d0b4004eb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675555080" }, { "r": "4.6.0", "os": "mac", "version": "1.11.0", "date": "2026-05-30T05:56:00.000Z", "arch": "aarch64", "commit": "2fea7dd47b04f2da7c94eccfe80d13485a7a90e6", "fileid": "3b696dc7263c8e2cb0684b383e521e19506947ada7f52644c5967ab4613d876c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675555080" }, { "r": "4.6.0", "os": "mac", "version": "1.11.0", "date": "2026-05-30T05:57:51.000Z", "arch": "x86_64", "commit": "2fea7dd47b04f2da7c94eccfe80d13485a7a90e6", "fileid": "c1e8067fa8537ef693fb50e3d37f9069a9579dedd78eb2003036f7ad1162ed2c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675555080" }, { "r": "4.7.0", "os": "win", "version": "1.11.0", "date": "2026-05-30T05:37:37.000Z", "arch": "x86_64", "commit": "2fea7dd47b04f2da7c94eccfe80d13485a7a90e6", "fileid": "09fba0b3d857a71f7cc5692890148f55bd257e3ac7c22997fd315117163c0bb4", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675555080" }, { "r": "4.5.3", "os": "win", "version": "1.11.0", "date": "2026-05-30T05:37:31.000Z", "arch": "x86_64", "commit": "2fea7dd47b04f2da7c94eccfe80d13485a7a90e6", "fileid": "29ec87f56f9fae098fcfa157c323347d7e337e9b2e526161046ddb4e878da8fd", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675555080" }, { "r": "4.6.0", "os": "win", "version": "1.11.0", "date": "2026-05-30T05:32:15.000Z", "arch": "x86_64", "commit": "2fea7dd47b04f2da7c94eccfe80d13485a7a90e6", "fileid": "adf6e52ac491c5d89f017cad68d3f7e1e5177708ead5a3fdf093baa94deea8c5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26675555080" } ] }