{ "_id": "6a1fdc9db401979e73438153", "Package": "GeneScape", "Type": "Package", "Title": "Simulate single cell and spatial transcriptomics data", "Version": "1.2", "Date": "2023-08-26", "Author": "Qi Gao", "Authors@R": "c(person(given = \"Qi\", family =\"Gao\", role = c(\"aut\", \"cre\"),\nemail = \"qi.gao@duke.edu\"))", "Maintainer": "Qi Gao ", "Description": "Simulate single cell and spatial transcriptomics data with\ncomplicated heterogeneity structure with or without reference\ndataset.", "Encoding": "UTF-8", "License": "GPL (>= 3)", "RoxygenNote": "6.0.1", "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nmake libssl-dev libproj-dev libsqlite3-dev libudunits2-dev\nlibnode-dev", "Repository": "https://qigao1.r-universe.dev", "Date/Publication": "2023-08-26 05:14:10 UTC", "RemoteUrl": "https://github.com/qigao1/genescape", "RemoteRef": "HEAD", "RemoteSha": "be6c631fd163574c860f9ba8df416e647e2c4276", "NeedsCompilation": "yes", "Packaged": { "Date": 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"qigao1", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_userbio": { "uuid": 38788608, "type": "user", "name": "qigao1" }, "_downloads": { "count": 120, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/GeneScape" }, "_devurl": "https://github.com/qigao1/genescape", "_searchresults": 2, "_topics": [ "cpp", "openmp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/GeneScape.html", "manual.pdf" ], "_homeurl": "https://github.com/qigao1/genescape", "_realowner": "qigao1", "_cranurl": true, "_releases": [ { "version": "1.0", "date": "2023-06-13" } ], "_exports": [ "add_distort", "aggregate_expression", "assign_cell_types", "assign_tissue_types", "cell_position_simulation", "changeLibSize", "cumsum_cpp", "downSampleRead", "est_bound", "estimate_gamma", "estimate_lognormal", "estimate_nb", "estimate_zinb", "estimate_zip", "fcsim", "GeneScape_est", "GeneScape_par", "GeneScape_sim", "GeneScapeS_est", "GeneScapeS_sim", "inverse_logit", "knn_tissue_update", "knnassign", "rotate_pg", "rotate_sample", "sample_int", "sample_region_simulation", "scale_sample", "shift_sample", "sp_dist_euclidean_cpp", "spot_simulate", "tissue_region_simulation", "update_sample_region", "zinb_nll" ], "_help": [ { "page": "add_distort", "title": "add_distort", "topics": [ "add_distort" ] }, { "page": "aggregate_expression", "title": "aggregate_expression", "topics": [ "aggregate_expression" ] }, { "page": "assign_cell_types", "title": "assign_cell_types", "topics": [ "assign_cell_types" ] }, { "page": "assign_tissue_types", "title": "assign_tissue_types", "topics": [ "assign_tissue_types" ] }, { "page": "cell_position_simulation", "title": "cell_position_simulation", "topics": [ "cell_position_simulation" ] }, { "page": "changeLibSize", "title": "changeLibSize This function modifies the simulated counts so that the total read count in each spot is the same as the example data.", "topics": [ "changeLibSize" ] }, { "page": "cumsum_cpp", "title": "cumsum_cpp This function calculates the cumulative sum (partial sum) of a vector.", "topics": [ "cumsum_cpp" ] }, { "page": "downSampleRead", "title": "downSampleRead This function uses down-sampling to obtain the reads in each spot.", "topics": [ "downSampleRead" ] }, { "page": "est_bound", "title": "est_bound", "topics": [ "est_bound" ] }, { "page": "estimate_gamma", "title": "estimate_gamma This function estimates gamma distribution shape and rate parameters.", "topics": [ "estimate_gamma" ] }, { "page": "estimate_lognormal", "title": "estimate_lognormal This function estimates estimate_lognormal distribution loc and scale parameters.", "topics": [ "estimate_lognormal" ] }, { "page": "estimate_nb", "title": "estimate_nb This function estimates negative binomial distribution mean and dispersion parameters.", "topics": [ "estimate_nb" ] }, { "page": "estimate_zinb", "title": "estimate_zinb This function estimates the mean, dispersion and zero inflation parameters in zero-inflated negative binomial distribution.", "topics": [ "estimate_zinb" ] }, { "page": "estimate_zip", "title": "estimate_zip", "topics": [ "estimate_zip" ] }, { "page": "fcsim", "title": "fcsim", "topics": [ "fcsim" ] }, { "page": "GeneScape_est", "title": "GeneScape_est", "topics": [ "GeneScape_est" ] }, { "page": "GeneScape_par", "title": "GeneScape_par", "topics": [ "GeneScape_par" ] }, { "page": "GeneScape_sim", "title": "GeneScape_sim", "topics": [ "GeneScape_sim" ] }, { "page": "GeneScapeS_est", "title": "GeneScapeS_est This function estimates distribution parameters from an example data.", "topics": [ "GeneScapeS_est" ] }, { "page": "GeneScapeS_sim", "title": "GeneScapeS_sim This function generates simulated data based on distribution parameters estimated from an example data.", "topics": [ "GeneScapeS_sim" ] }, { "page": "inverse_logit", "title": "inverse_logit This function is the inverse logit function.", "topics": [ "inverse_logit" ] }, { "page": "knn_tissue_update", "title": "knn_tissue_update", "topics": [ "knn_tissue_update" ] }, { "page": "knnassign", "title": "knnassign This function uses KNN sampling to simulate gradually changed tissue types.", "topics": [ "knnassign" ] }, { "page": "rotate_pg", "title": "rotate_pg", "topics": [ "rotate_pg" ] }, { "page": "rotate_sample", "title": "rotate_sample", "topics": [ "rotate_sample" ] }, { "page": "sample_int", "title": "sample_int This function samples integers from 1 to an upper limit integer value with equal probability without replacement.", "topics": [ "sample_int" ] }, { "page": "sample_region_simulation", "title": "sample_region_simulation", "topics": [ "sample_region_simulation" ] }, { "page": "scale_sample", "title": "scale_sample", "topics": [ "scale_sample" ] }, { "page": "shift_sample", "title": "shift_sample", "topics": [ "shift_sample" ] }, { "page": "sp_dist_euclidean_cpp", "title": "sp_dist_euclidean_cpp This function calculates Euclidean distance between cell locations and spot locations.", "topics": [ "sp_dist_euclidean_cpp" ] }, { "page": "spot_simulate", "title": "spot_simulate", "topics": [ "spot_simulate" ] }, { "page": "tissue_region_simulation", "title": "tissue_region_simulation", "topics": [ "tissue_region_simulation" ] }, { "page": "update_sample_region", "title": "update_sample_region", "topics": [ "update_sample_region" ] }, { "page": "zinb_nll", "title": "zinb_nll This function calculates the negative log likelihood of zero-inflated negative binomial distribution.", "topics": [ "zinb_nll" ] } ], "_rundeps": [ "class", "classInt", "concaveman", "corpcor", "curl", "DBI", "e1071", "jsonlite", "KernSmooth", "lamW", "MASS", "proxy", "Rcpp", "RcppArmadillo", "RcppParallel", "s2", "sf", "units", "V8", "wk" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": 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