{ "_id": "6a1f25f6b401979e73421bc2", "Package": "SiFINeT", "Type": "Package", "Title": "Single Cell Feature Identification with Network Topology", "Version": "1.13", "Date": "2025-01-01", "Author": "Qi Gao [aut, cre]", "Maintainer": "Qi Gao ", "Authors@R": "person(given = \"Qi\",\nfamily = \"Gao\",\nrole = c(\"aut\", \"cre\"),\nemail = \"gqi@med.umich.edu\")", "Description": "Cluster-independent method based on topology structure of\ngene co-expression network for identifying feature gene sets,\nextracting cellular subpopulations, and elucidating intrinsic\nrelationships among these subpopulations. Without prior cell\nclustering, SifiNet circumvents potential inaccuracies in\nclustering that may influence subsequent analyses. This method\nis introduced in Qi Gao, Zhicheng Ji, Liuyang Wang, Kouros\nOwzar, Qi-Jing Li, Cliburn Chan, Jichun Xie \"SifiNet: a robust\nand accurate method to identify feature gene sets and annotate\ncells\" (2024) .", "License": "GPL-3", "Encoding": "UTF-8", "RoxygenNote": "7.3.1", "NeedsCompilation": "yes", "BuildVignettes": "yes", "VignetteBuilder": "knitr", "Packaged": { "Date": "2026-05-16 05:59:52 UTC", "User": "root" }, "Repository": "https://cran.r-universe.dev", "Date/Publication": "2025-01-16 15:10:05 UTC", "RemoteUrl": "https://github.com/cran/SiFINeT", "RemoteRef": "HEAD", "RemoteSha": "2981dc15864a327aeac7d5ae109f102f7fb99426", "MD5sum": "b2f227083617979ce3ed9edd5e4ca68a", "_user": "cran", "_type": "src", "_file": "SiFINeT_1.13.tar.gz", "_fileid": "35ccef879062c0d9fa73b53045da8a218adf657b8f719c04539d327e5614917d", "_filesize": 2852472, "_sha256": "35ccef879062c0d9fa73b53045da8a218adf657b8f719c04539d327e5614917d", "_created": "2026-05-16T05:59:52.000Z", "_published": 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"2981dc15864a327aeac7d5ae109f102f7fb99426", "author": "Qi Gao ", "committer": "cran-robot ", "message": "version 1.13\n", "time": 1737040205 }, "_maintainer": { "name": "Qi Gao", "email": "gqi@med.umich.edu" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6.0", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "utils", "role": "Depends" }, { "package": "stats", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 1.0.9", "role": "Imports" }, { "package": "quantreg", "version": ">= 5.94", "role": "Imports" }, { "package": "igraph", "version": ">= 1.3.5", "role": "Imports" }, { "package": "Matrix", "version": ">= 1.5-1", "role": "Imports" }, { "package": "ggraph", "version": ">= 2.0.6", "role": "Imports" }, { "package": "ggplot2", "version": ">= 3.3.6", "role": "Imports" }, { "package": "rmarkdown", "version": ">= 2.20", "role": 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"enrich_feature_set", "EstNull", "extract_subnetwork", "feature_coexp", "filter_lowexp", "find_unique_feature", "geneset_topology", "norm_FDR_SQAUC", "quantile_thres" ], "_help": [ { "page": "assign_shared_feature", "title": "assign_shared_feature", "topics": [ "assign_shared_feature" ] }, { "page": "cal_coexp", "title": "cal_coexp This function calculates the coexpression patterns between genes and returns the coexpression matrix.", "topics": [ "cal_coexp" ] }, { "page": "cal_coexp_sp", "title": "cal_coexp_sp This function calculates the coexpression patterns between genes in sparse matrix and returns the coexpression matrix.", "topics": [ "cal_coexp_sp" ] }, { "page": "cal_conn", "title": "cal_conn This function calculates the first 3 order connectivities for each gene and returns the list of vectors of connectivities.", "topics": [ "cal_conn" ] }, { "page": "cal_connectivity", "title": "cal_connectivity", "topics": [ "cal_connectivity" ] }, { "page": "create_network", "title": "create_network", "topics": [ "create_network" ] }, { "page": "create_SiFINeT_object", "title": "create_SiFINeT_object", "topics": [ "create_SiFINeT_object" ] }, { "page": "enrich_feature_set", "title": "enrich_feature_set", "topics": [ "enrich_feature_set" ] }, { "page": "EstNull", "title": "EstNull This function is a Rcpp version of Wenguang Sun and Tony T. Cai's EstNull.func R function, estimating null distribution from data. Sun, W., & Cai, T. T. (2007). Oracle and Adaptive Compound Decision Rules for False Discovery Rate Control. Journal of the American Statistical Association, 102(479), 901–912.", "topics": [ "EstNull" ] }, { "page": "extract_subnetwork", "title": "extract_subnetwork", "topics": [ "extract_subnetwork" ] }, { "page": "feature_coexp", "title": "feature_coexp", "topics": [ "feature_coexp" ] }, { "page": "filter_lowexp", "title": "filter_lowexp", "topics": [ "filter_lowexp" ] }, { "page": "find_unique_feature", "title": "find_unique_feature", "topics": [ "find_unique_feature" ] }, { "page": "geneset_topology", "title": "geneset_topology", "topics": [ "geneset_topology" ] }, { "page": "norm_FDR_SQAUC", "title": "norm_FDR_SQAUC The function controls the false discovery rate (FDR) of coexpression patterns using SQAUC method Jichun Xie and Ruosha Li. \"False discovery rate control for high dimensional networks of quantile associations conditioning on covariates\". In: J R Stat Soc Series B Stat Methodol (2018). doi: 10.1111/rssb.12288.", "topics": [ "norm_FDR_SQAUC" ] }, { "page": "quantile_thres", "title": "quantile_thres", "topics": [ "quantile_thres" ] }, { "page": "SiFINeT-class", "title": "The SiFINeT Class", "topics": [ "SiFINeT", "SiFINeT-class" ] } ], "_readme": "https://github.com/cran/SiFINeT/raw/HEAD/README.md", "_rundeps": [ "base64enc", "cachem", "cli", "cpp11", "dplyr", "farver", "fastmap", "generics", "ggforce", "ggplot2", "ggraph", "ggrepel", "glue", "graphlayouts", "gridExtra", "gtable", "igraph", "isoband", "jsonlite", "labeling", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "MatrixModels", "memoise", "pillar", "pkgconfig", "polyclip", "purrr", "quantreg", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "rlang", "S7", "scales", "SparseM", "stringi", "stringr", "survival", "systemfonts", "tibble", "tidygraph", "tidyr", "tidyselect", "tweenr", "utf8", "vctrs", "viridis", "viridisLite", "withr" ], "_sysdeps": [ { "shlib": "libblas", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.26+ds-1ubuntu0.1", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" }, { "shlib": "libgomp", "package": "libgomp1", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "openmp", "homepage": "http://gcc.gnu.org/", "description": "GCC OpenMP (GOMP) support library" } ], "_vignettes": [ { "source": "SifiNet_tutorial.Rmd", "filename": "SifiNet_tutorial.html", "title": "Introduction to SifiNet", "author": "Qi Gao", "engine": "knitr::rmarkdown", "headings": [ "Installation", "SifiNet method", "Create SifiNet object", "Section A: Construct the gene co-expression network", "Section B: Calculate gene connectivity and find feature gene sets", "Session information" ], "created": "2025-01-16 15:10:05", "modified": "2025-01-16 15:10:05", "commits": 1 } ], "_score": 2.8750612633917, "_indexed": true, "_nocasepkg": "sifinet", "_universes": [ "cran" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.13", "date": "2026-05-16T06:02:27.000Z", "distro": "noble", "arch": "aarch64", "commit": "2981dc15864a327aeac7d5ae109f102f7fb99426", "fileid": "b3b2fca20b4701198b60b7f6b01ca4c053b6b76007cbd9827b798a1980982ef2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/25954377615" }, { "r": "4.7.0", "os": "linux", "version": "1.13", "date": "2026-05-16T06:02:33.000Z", "distro": "noble", "arch": "x86_64", "commit": "2981dc15864a327aeac7d5ae109f102f7fb99426", "fileid": "f2d7294c56a65a8d3a9610e574073108ca67f53356f5b18e91f331027bd57e69", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/25954377615" }, { "r": "4.6.0", "os": "linux", "version": "1.13", "date": "2026-05-16T06:02:27.000Z", "distro": "noble", "arch": "aarch64", "commit": "2981dc15864a327aeac7d5ae109f102f7fb99426", "fileid": "26f2c9f7cdcd2025ff5e3471dd37d314f08b1e54903d86f019a5870af3c88ca2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/25954377615" }, { "r": "4.6.0", "os": "linux", "version": "1.13", "date": "2026-05-16T06:03:17.000Z", "distro": "noble", "arch": "x86_64", "commit": "2981dc15864a327aeac7d5ae109f102f7fb99426", "fileid": "d8ce9dd630581bbb25dd92a7a6275c49e5e4c702579ff2a83376866feea37a46", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/25954377615" }, { "r": "4.6.0", "os": "wasm", "version": "1.13", "date": "2026-06-02T18:49:45.000Z", "arch": "emscripten", "commit": "2981dc15864a327aeac7d5ae109f102f7fb99426", "fileid": "2508e66d894a2dfa53842f53eba21f28e52bebc3ede1164631fee80ab069b397", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/25954377615" } ] }