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Merge branch 'master' of github.com:stemangiola/sccomp # Conflicts: # DESCRIPTION
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@@ -6,19 +6,17 @@ Authors@R: c(person("Stefano", "Mangiola", email = "[email protected]", | |
| ) | ||
| Description: A robust and outlier-aware method for testing differential tissue composition from single-cell data. This model can infer changes in tissue composition and heterogeneity, and can produce realistic data simulations based on any existing dataset. This model can also transfer knowledge from a large set of integrated datasets to increase accuracy further. | ||
| License: GPL-3 | ||
| URL: https://github.com/MangiolaLaboratory/sccomp | ||
| BugReports: https://github.com/MangiolaLaboratory/sccomp/issues | ||
| Encoding: UTF-8 | ||
| LazyData: true | ||
| Roxygen: list(markdown = TRUE) | ||
| RoxygenNote: 7.3.1 | ||
| Biarch: true | ||
| Depends: | ||
| R (>= 4.2.0) | ||
| Imports: | ||
| methods, | ||
| Rcpp (>= 0.12.0), | ||
| RcppParallel (>= 5.0.1), | ||
| rstantools (>= 2.1.1), | ||
| rstan (>= 2.26.0), | ||
| RoxygenNote: 7.3.2 | ||
| Depends: R (>= 4.2.0) | ||
| Imports: | ||
| instantiate (>= 0.2.3), | ||
| callr, | ||
| fs, | ||
| stats, | ||
| SeuratObject, | ||
| SingleCellExperiment, | ||
| parallel, | ||
|
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@@ -40,44 +38,28 @@ Imports: | |
| readr, | ||
| scales, | ||
| stringr, | ||
| glue | ||
| glue, | ||
| withr, | ||
| digest | ||
| Suggests: | ||
| cmdstanr (>= 0.6.0), | ||
| knitr, | ||
| rmarkdown, | ||
| BiocStyle, | ||
| testthat (>= 3.0.0), | ||
| markdown, | ||
| knitr, | ||
| loo, | ||
| prettydoc, | ||
| tidyseurat, | ||
| tidySingleCellExperiment, | ||
| prettydoc | ||
| Enhances: | ||
| furrr, | ||
| extraDistr | ||
| LinkingTo: | ||
| BH (>= 1.66.0), | ||
| Rcpp (>= 0.12.0), | ||
| RcppEigen (>= 0.3.3.3.0), | ||
| RcppParallel (>= 5.0.1), | ||
| rstan (>= 2.26.0), | ||
| StanHeaders (>= 2.26.0) | ||
| SystemRequirements: GNU make | ||
| VignetteBuilder: | ||
| knitr | ||
| RdMacros: | ||
| lifecycle | ||
| biocViews: | ||
| ImmunoOncology, | ||
| Normalization, | ||
| Sequencing, | ||
| RNASeq, | ||
| Software, | ||
| GeneExpression, | ||
| Transcriptomics, | ||
| SingleCell, | ||
| Clustering | ||
| LazyDataCompression: xz | ||
| Config/testthat/edition: 3 | ||
| URL: https://github.com/stemangiola/sccomp | ||
| BugReports: https://github.com/stemangiola/sccomp/issues | ||
| bayesplot, | ||
| posterior | ||
| Remotes: | ||
| wlandau/instantiate | ||
| Additional_repositories: | ||
| https://mc-stan.org/r-packages/ | ||
| SystemRequirements: CmdStan (https://mc-stan.org/users/interfaces/cmdstan) | ||
| biocViews: Bayesian, Regression, DifferentialExpression, SingleCell | ||
| LazyData: true | ||
| VignetteBuilder: knitr | ||
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| sample_safe <- function(model, fx, ...) { | ||
| tryCatch( | ||
| { | ||
| # Attempt to run the arbitrary fx with additional arguments | ||
| result <- fx(model, ...) | ||
| return(result) | ||
| }, | ||
| error = function(e) { | ||
| # Check if the error message is "model not compiled" | ||
| if (grepl("Model not compiled", e$message)) { | ||
| message("Model not compiled. Compiling.") | ||
| # Load the model with force=TRUE | ||
| model <- model$compile(cpp_options = list(stan_threads = TRUE)) # load_model("glm_multi_beta_binomial_generate_data", force = TRUE) | ||
| # Retry the arbitrary fx with additional arguments | ||
| result <- fx(model, ...) | ||
| return(result) | ||
| } else { | ||
| # If a different error, rethrow the error | ||
| stop(e) | ||
| } | ||
| } | ||
| ) | ||
| } | ||
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| sample_fx <- function(model, ...) { | ||
| model$sample(...) | ||
| } | ||
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| pathfinder_fx <- function(model, ...) { | ||
| model$pathfinder(...) | ||
| } | ||
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| variational_fx <- function(model, ...) { | ||
| model$variational(...) | ||
| } | ||
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| generate_quantities_fx <- function(model, ...) { | ||
| model$generate_quantities(...) | ||
| } |
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