{ "_id": "6a153deeacfb0bcc41d54d42", "Package": "TorchDecon", "Type": "Package", "Title": "Deep Learning-Based Cell Type Deconvolution Using torch", "Version": "1.0.0", "Date": "2026-01-26", "Authors@R": "person(\"Zaoqu\", \"Liu\", email = \"liuzaoqu@163.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-0452-742X\"))", "Description": "A deep neural network ensemble approach for cell type\ndeconvolution of bulk RNA-seq data. TorchDecon uses simulated\nbulk samples generated from single-cell RNA-seq data to train\ndeep neural networks that predict cell type fractions. This\npackage is an R-native implementation based on the Scaden\nalgorithm, built on the torch framework (LibTorch C++ backend)\nfor GPU acceleration and cross-platform compatibility.\nSeamlessly integrates with Seurat objects (v4 and v5\ncompatible).", "License": "MIT + file LICENSE", "URL": "https://github.com/Zaoqu-Liu/TorchDecon", "BugReports": "https://github.com/Zaoqu-Liu/TorchDecon/issues", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev python3 zlib1g-dev", "Repository": "https://zaoqu-liu.r-universe.dev", "Date/Publication": "2026-01-26 02:33:01 UTC", "RemoteUrl": "https://github.com/Zaoqu-Liu/TorchDecon", "RemoteRef": "main", "RemoteSha": "139bac3eecffa73b3f979e2a96463fa13f6f05f6", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-26 06:24:28 UTC", "User": "root" }, "Author": "Zaoqu Liu [aut, cre] (ORCID: )", "Maintainer": "Zaoqu Liu ", "MD5sum": "dda3edb3ff3d8038aa76d136f4ebd7ea", "_user": "zaoqu-liu", "_type": "src", "_file": "TorchDecon_1.0.0.tar.gz", "_fileid": "ee72502b552fb36b9f757243f045ac97c224e22e8a2a83af056096101dcf5502", "_filesize": 234821, "_sha256": "ee72502b552fb36b9f757243f045ac97c224e22e8a2a83af056096101dcf5502", "_created": "2026-05-26T06:24:28.000Z", "_published": "2026-05-26T06:30:06.624Z", "_distro": "noble", "_jobs": [ { "job": 77819069639, "time": 287, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7210311663" }, { "job": 77819069651, "time": 283, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7210309922" }, { "job": 77819069628, "time": 166, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7210283653" }, { "job": 77819069654, "time": 175, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7210290925" }, { "job": 77818566992, "time": 266, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7210242485" }, { "job": 77819069632, "time": 182, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7210285161" }, { "job": 77819069671, "time": 239, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7210299971" }, { "job": 77819069715, "time": 227, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7210296715" }, { "job": 77819069704, "time": 231, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7210297538" } ], "_buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26435882733", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/Zaoqu-Liu/TorchDecon", "_commit": { "id": "139bac3eecffa73b3f979e2a96463fa13f6f05f6", "author": "Zaoqu-Liu ", "committer": "Zaoqu-Liu ", "message": "docs: Add evaluation function documentation pages\n", "time": 1769394781 }, "_maintainer": { "name": "Zaoqu Liu", "email": "liuzaoqu@163.com", "login": "zaoqu-liu", "orcid": "0000-0002-0452-742X", "description": "AI4S", "uuid": 68080738 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "torch", "version": ">= 0.9.0", "role": "Imports" }, { "package": "Seurat", "version": ">= 4.0.0", "role": "Imports" }, { "package": "SeuratObject", "version": ">= 4.0.0", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "future", "role": "Imports" }, { "package": "future.apply", "role": "Imports" }, { "package": "progressr", "role": "Imports" }, { "package": "cli", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "Rcpp", "role": "Suggests" } ], "_owner": "zaoqu-liu", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-04", "n": 6 }, { "week": "2026-05", "n": 5 } ], "_tags": [], "_stars": 1, "_contributors": [ { "user": "zaoqu-liu", "count": 11, "uuid": 68080738 } ], "_userbio": { "uuid": 68080738, "type": "user", "name": "LIU Zaoqu", "description": "AI4S" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/TorchDecon" }, "_devurl": "https://github.com/zaoqu-liu/torchdecon", "_searchresults": 5, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "extra/TorchDecon.html", "manual.pdf" ], "_cranurl": false, "_exports": [ "ApplyScaling", "CalculateAccuracy", "CalculateCorrelation", "CalculateMAE", "CalculateMRE", "CalculateRMSE", "CreateTorchDecon", "CreateTorchDeconEnsemble", "EvaluateDeconvolution", "EvaluatePredictions", "ExportSimulation", "ExtractCellTypes", "ExtractSeuratData", "GenerateExampleData", "GetTrainingHistory", "LoadModel", "MergeSimulations", "PlotEvaluation", "PlotTrainingHistory", "PredictFractions", "ProcessPredictionData", "ProcessTrainingData", "QuickPredict", "RunTorchDecon", "SaveModel", "SimulateBulk", "SimulationToDataFrame", "TrainModel" ], "_help": [ { "page": "ApplyScaling", "title": "Apply Scaling to New Data", "topics": [ "ApplyScaling" ] }, { "page": "CalculateAccuracy", "title": "Calculate Accuracy", "topics": [ "CalculateAccuracy" ] }, { "page": "CalculateCorrelation", "title": "Calculate Correlation", "topics": [ "CalculateCorrelation" ] }, { "page": "CalculateMAE", "title": "Calculate MAE", "topics": [ "CalculateMAE" ] }, { "page": "CalculateMRE", "title": "Calculate MRE", "topics": [ "CalculateMRE" ] }, { "page": "CalculateRMSE", "title": "Calculate RMSE", "topics": [ "CalculateRMSE" ] }, { "page": "CreateTorchDecon", "title": "Create TorchDecon Model", "topics": [ "CreateTorchDecon" ] }, { "page": "CreateTorchDeconEnsemble", "title": "Create TorchDecon Ensemble", "topics": [ "CreateTorchDeconEnsemble" ] }, { "page": "EvaluateDeconvolution", "title": "Evaluate Deconvolution Results", "topics": [ "EvaluateDeconvolution" ] }, { "page": "EvaluatePredictions", "title": "Evaluate Predictions", "topics": [ "EvaluatePredictions" ] }, { "page": "ExportSimulation", "title": "Export Simulation to Files", "topics": [ "ExportSimulation" ] }, { "page": "ExtractCellTypes", "title": "Extract Cell Type Labels from Seurat Object", "topics": [ "ExtractCellTypes" ] }, { "page": "ExtractSeuratData", "title": "Extract Count Matrix from Seurat Object", "topics": [ "ExtractSeuratData" ] }, { "page": "GenerateExampleData", "title": "Generate Example Data", "topics": [ "GenerateExampleData" ] }, { "page": "GetTrainingHistory", "title": "Get Training History", "topics": [ "GetTrainingHistory" ] }, { "page": "LoadModel", "title": "Load TorchDecon Model", "topics": [ "LoadModel" ] }, { "page": "MergeSimulations", "title": "Merge Simulations", "topics": [ "MergeSimulations" ] }, { "page": "PlotEvaluation", "title": "Plot Evaluation Results", "topics": [ "PlotEvaluation" ] }, { "page": "PlotTrainingHistory", "title": "Plot Training History", "topics": [ "PlotTrainingHistory" ] }, { "page": "PredictFractions", "title": "Predict Cell Type Fractions", "topics": [ "PredictFractions" ] }, { "page": "print.TorchDeconEnsemble", "title": "Print Method for TorchDeconEnsemble", "topics": [ "print.TorchDeconEnsemble" ] }, { "page": "print.TorchDeconEvaluation", "title": "Print Method for TorchDeconEvaluation", "topics": [ "print.TorchDeconEvaluation" ] }, { "page": "print.TorchDeconModel", "title": "Print Method for TorchDeconModel", "topics": [ "print.TorchDeconModel" ] }, { "page": "print.TorchDeconProcessed", "title": "Print Method for TorchDeconProcessed", "topics": [ "print.TorchDeconProcessed" ] }, { "page": "print.TorchDeconSimulation", "title": "Print Method for TorchDeconSimulation", "topics": [ "print.TorchDeconSimulation" ] }, { "page": "ProcessPredictionData", "title": "Process Prediction Data", "topics": [ "ProcessPredictionData" ] }, { "page": "ProcessTrainingData", "title": "Process Training Data for TorchDecon", "topics": [ "ProcessTrainingData" ] }, { "page": "QuickPredict", "title": "Quick Prediction with Pre-trained Model", "topics": [ "QuickPredict" ] }, { "page": "RunTorchDecon", "title": "Run Complete TorchDecon Workflow", "topics": [ "RunTorchDecon" ] }, { "page": "SaveModel", "title": "Save TorchDecon Model", "topics": [ "SaveModel" ] }, { "page": "seurat-utils", "title": "Seurat Compatibility Utilities", "topics": [ "seurat-utils" ] }, { "page": "SimulateBulk", "title": "Simulate Bulk RNA-seq Data from Single-Cell Data", "topics": [ "SimulateBulk" ] }, { "page": "SimulationToDataFrame", "title": "Convert Simulation to Data Frame", "topics": [ "SimulationToDataFrame" ] }, { "page": "summary.TorchDeconEvaluation", "title": "Summary Method for TorchDeconEvaluation", "topics": [ "summary.TorchDeconEvaluation" ] }, { "page": "summary.TorchDeconModel", "title": "Summary Method for TorchDeconModel", "topics": [ "summary.TorchDeconModel" ] }, { "page": "TrainModel", "title": "Train TorchDecon Model", "topics": [ "TrainModel" ] } ], "_readme": "https://github.com/Zaoqu-Liu/TorchDecon/raw/main/README.md", "_rundeps": [ "abind", "askpass", "base64enc", "BH", "bit", "bit64", "bitops", "bslib", "cachem", "callr", "caTools", "cli", "cluster", "codetools", "commonmark", "coro", "cowplot", "cpp11", "crosstalk", "curl", "data.table", "deldir", "desc", "digest", "dotCall64", "dplyr", "dqrng", "evaluate", "farver", "fastDummies", "fastmap", "fitdistrplus", "FNN", "fontawesome", "fs", "future", "future.apply", "generics", "ggplot2", "ggrepel", "ggridges", "globals", "glue", "goftest", "gplots", "gridExtra", "gtable", "gtools", "here", "highr", "htmltools", "htmlwidgets", "httpuv", "httr", "ica", "igraph", "irlba", "isoband", "jquerylib", "jsonlite", "KernSmooth", "knitr", "labeling", "later", "lattice", "lazyeval", "lifecycle", "listenv", "lmtest", "magrittr", "MASS", "Matrix", "matrixStats", "memoise", "mime", "miniUI", "nlme", "openssl", "otel", "parallelly", "patchwork", "pbapply", "pillar", "pkgconfig", "plotly", "plyr", "png", "polyclip", "processx", "progressr", "promises", "ps", "purrr", "R6", "RANN", "rappdirs", "RColorBrewer", "Rcpp", "RcppAnnoy", "RcppArmadillo", "RcppEigen", "RcppHNSW", "RcppProgress", "RcppTOML", "reshape2", "reticulate", "rlang", "rmarkdown", "ROCR", "rprojroot", "RSpectra", "Rtsne", "S7", "safetensors", "sass", "scales", "scattermore", "sctransform", "Seurat", "SeuratObject", "shiny", "sitmo", "sourcetools", "sp", "spam", "spatstat.data", "spatstat.explore", "spatstat.geom", "spatstat.random", "spatstat.sparse", "spatstat.univar", "spatstat.utils", "stringi", "stringr", "survival", "sys", "tensor", "tibble", "tidyr", "tidyselect", "tinytex", "torch", "utf8", "uwot", "vctrs", "viridisLite", "withr", "xfun", "xtable", "yaml", "zoo" ], "_vignettes": [ { "source": "advanced-usage.Rmd", "filename": "advanced-usage.html", "title": "Advanced Usage and Best Practices", "author": "Zaoqu Liu", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "GPU Acceleration", "Checking GPU Availability", "Specifying Device", "Custom Model Architectures", "Creating Custom Networks", "Architecture Selection Guidelines", "Training Optimization", "Early Stopping", "Learning Rate Tuning", "Batch Size Considerations", "Data Quality Optimization", "Handling Unknown Cell Types", "Optimal Sample Simulation", "Gene Selection Strategies", "Working with Multiple Datasets", "Merging Simulations", "Cross-validation Strategy", "Model Persistence and Deployment", "Saving Models with Metadata", "Loading and Deploying", "Troubleshooting", "Common Issues and Solutions", "Memory Management", "Reproducibility", "Setting Seeds", "Best Practices Summary" ], "created": "2026-01-26 02:10:18", "modified": "2026-01-26 02:10:18", "commits": 1 }, { "source": "algorithm-details.Rmd", "filename": "algorithm-details.html", "title": "Algorithm and Mathematical Framework", "author": "Zaoqu Liu", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Problem Formulation", "The Deconvolution Problem", "Traditional Approaches vs. Deep Learning", "Algorithmic Pipeline", "Overview", "Step 1: Bulk RNA-seq Simulation", "Mathematical Formulation", "Sparse Sample Generation", "Step 2: Data Preprocessing", "Log Transformation", "Sample-wise Min-Max Normalization", "Gene Filtering", "Step 3: Neural Network Architecture", "Fully Connected Network", "Output Layer (Softmax)", "Dropout Regularization", "Step 4: Training", "Loss Function", "Adam Optimizer", "Step 5: Ensemble Prediction", "Architecture Specifications", "Theoretical Considerations", "Universal Approximation", "Advantages over Linear Models", "Limitations", "References" ], "created": "2026-01-26 02:10:18", "modified": "2026-01-26 02:10:18", "commits": 1 }, { "source": "TorchDecon-introduction.Rmd", "filename": "TorchDecon-introduction.html", "title": "Introduction to TorchDecon", "author": "Zaoqu Liu", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Key Features", "Installation", "Quick Start", "Step-by-Step Workflow", "Step 1: Simulate Bulk Data", "Step 2: Process Training Data", "Step 3: Create and Train Model", "Step 4: Predict Cell Fractions", "Step 5: Save and Load Model", "Model Architecture", "Evaluation", "Tips for Best Results", "Citation", "Session Info" ], "created": "2026-01-25 18:37:08", "modified": "2026-01-25 18:37:08", "commits": 1 }, { "source": "visualization-tutorial.Rmd", "filename": "visualization-tutorial.html", "title": "Visualization and Result Interpretation", "author": "Zaoqu Liu", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Setup", "Generate Example Data and Run Deconvolution", "Visualization Methods", "1. Stacked Bar Plot", "2. Heatmap Visualization", "3. Box Plot Comparison", "4. Training History Plot", "5. Correlation Plot (with Ground Truth)", "6. Per-Cell Type Accuracy", "7. Pie Chart for Individual Samples", "Advanced Visualization", "Ensemble Model Comparison", "Summary" ], "created": "2026-01-26 02:10:18", "modified": "2026-01-26 02:10:18", "commits": 1 } ], "_score": 3.6020599913279625, "_indexed": true, "_nocasepkg": "torchdecon", "_universes": [ "zaoqu-liu" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.0", "date": "2026-05-26T06:27:53.000Z", "distro": "noble", "commit": "139bac3eecffa73b3f979e2a96463fa13f6f05f6", "fileid": "8a77a823e967d8fd952cda83b1839b04f58f6c79ac63ed9691f85a5636766b9e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26435882733" }, { "r": "4.6.0", "os": "linux", "version": "1.0.0", "date": "2026-05-26T06:28:09.000Z", "distro": "noble", "commit": "139bac3eecffa73b3f979e2a96463fa13f6f05f6", "fileid": "765978031f28c3744874f0877910f2a85b8916a967d07bc29af1d59bb33a0012", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26435882733" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0", "date": "2026-05-26T06:26:32.000Z", "commit": "139bac3eecffa73b3f979e2a96463fa13f6f05f6", "fileid": "d476cc105fdc5a8d66f1c9e691ce77b356123b86848f0991ce913c75cc73fad8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26435882733" }, { "r": "4.6.0", "os": "mac", "version": "1.0.0", "date": "2026-05-26T06:26:58.000Z", "commit": "139bac3eecffa73b3f979e2a96463fa13f6f05f6", "fileid": "70eaaad79f38a75f4cf1085ac15f88780f1195f64719177e2ce1b0e3db8c43e5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26435882733" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.0", "date": "2026-05-26T06:27:57.000Z", "commit": "139bac3eecffa73b3f979e2a96463fa13f6f05f6", "fileid": "29778e94525010cee86931fdc69a2e2e101aa7e7365d2c68c402ce325835d244", "status": "success", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26435882733" }, { "r": "4.7.0", "os": "win", "version": "1.0.0", "date": "2026-05-26T06:27:05.000Z", "commit": "139bac3eecffa73b3f979e2a96463fa13f6f05f6", "fileid": "2bc7db8eaa4ac7aa52dfcc91ef8eea0aac5a1bc40f90db45eb9a5c73f4c99faa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26435882733" }, { "r": "4.5.3", "os": "win", "version": "1.0.0", "date": "2026-05-26T06:26:35.000Z", "commit": "139bac3eecffa73b3f979e2a96463fa13f6f05f6", "fileid": "efd1fd41c20c578dba99bc191170652c4fb6feeed8baa1b301d757806a20ce71", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26435882733" }, { "r": "4.6.0", "os": "win", "version": "1.0.0", "date": "2026-05-26T06:26:32.000Z", "commit": "139bac3eecffa73b3f979e2a96463fa13f6f05f6", "fileid": "cf10729d6ef6b3150720ebcf5f802e61acad29b898a38366a4e469d26c9b7081", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/zaoqu-liu/actions/runs/26435882733" } ] }