{ "_id": "6a16966eacfb0bcc41d7ba2f", "Package": "PLEXI", "Type": "Package", "Title": "Multiplex Network Analysis", "Version": "1.0.0", "Authors@R": "c(person(\"Behnam\", \"Yousefi\", role = c(\"aut\", \"cre\",\"cph\"),\nemail = \"yousefi.bme@gmail.com\"),\nperson(\"Farzaneh\", \"Firoozbakht\", role = \"aut\"))", "Description": "Interactions between different biological entities are\ncrucial for the function of biological systems. In such\nnetworks, nodes represent biological elements, such as genes,\nproteins and microbes, and their interactions can be defined by\nedges, which can be either binary or weighted. The\ndysregulation of these networks can be associated with\ndifferent clinical conditions such as diseases and response to\ntreatments. However, such variations often occur locally and do\nnot concern the whole network. To capture local variations of\nsuch networks, we propose multiplex network differential\nanalysis (MNDA). MNDA allows to quantify the variations in the\nlocal neighborhood of each node (e.g. gene) between the two\ngiven clinical states, and to test for statistical significance\nof such variation. Yousefi et al. (2023)\n.", "License": "GPL (>= 3)", "Encoding": "UTF-8", "RoxygenNote": "7.2.3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-27 06:55:40 UTC", "User": "root" }, "Author": "Behnam Yousefi [aut, cre, cph], Farzaneh Firoozbakht [aut]", "Maintainer": "Behnam Yousefi ", "Config/pak/sysreqs": "libfontconfig1-dev libfreetype6-dev libglpk-dev\nlibicu-dev libpng-dev libxml2-dev python3", "Repository": "https://behnam-yousefi.r-universe.dev", "Date/Publication": "2023-08-09 16:38:54 UTC", "RemoteUrl": "https://github.com/cran/PLEXI", "RemoteRef": "HEAD", "RemoteSha": "4bf3883e0614f4aa93995c96b3bab1e59c87662b", "MD5sum": "54d070ef52a24949a1e8e5e94cf6f06e", "_user": "behnam-yousefi", "_type": "src", "_file": "PLEXI_1.0.0.tar.gz", "_fileid": "13bff38357626c7f0085469793cff2c4df6d821da229651646aaf8581ce505c7", "_filesize": 135276, "_sha256": "13bff38357626c7f0085469793cff2c4df6d821da229651646aaf8581ce505c7", "_created": "2026-05-27T06:55:40.000Z", "_published": "2026-05-27T06:59:58.577Z", "_distro": "noble", "_jobs": [ { "job": 78023884456, "time": 135, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7233871649" }, { "job": 78023884519, "time": 131, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7233870948" }, { "job": 78023884450, "time": 73, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7233875538" }, { "job": 78023884500, "time": 113, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7233896181" }, { "job": 78023442033, "time": 203, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7233834188" }, { "job": 78023884472, "time": 104, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7233863234" }, { "job": 78023884609, "time": 72, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7233854779" }, { "job": 78023884502, "time": 73, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7233854887" }, { "job": 78023884492, "time": 82, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7233856971" } ], "_buildurl": "https://github.com/r-universe/behnam-yousefi/actions/runs/26447429749", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/PLEXI", "_commit": { "id": "4bf3883e0614f4aa93995c96b3bab1e59c87662b", "author": "Behnam Yousefi ", "committer": "cran-robot ", "message": "version 1.0.0\n", "time": 1691599134 }, "_maintainer": { "name": "Behnam Yousefi", "email": "yousefi.bme@gmail.com", "login": "behnam-yousefi", "linkedin": "in/behnam-yousefi-bme", "twitter": "@behnam_bme", "description": "I am a researcher in the field of network medicine.", "uuid": 46751569 }, "_registered": true, "_dependencies": [ { "package": "assertthat", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "keras", "role": "Imports" }, { "package": "ggraph", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "aggregation", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "graphics", "role": "Imports" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_contributors": [ { "user": "behnam-yousefi", "count": 1, "uuid": 46751569 } ], "_userbio": { "uuid": 46751569, "type": "user", "name": "Behnam Yousefi", "description": "I am a researcher in the field of network medicine." }, "_downloads": { "count": 159, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/PLEXI" }, "_searchresults": 5, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/PLEXI.html", "manual.pdf" ], "_realowner": "behnam-yousefi", "_cranurl": false, "_releases": [ { "version": "1.0.0", "date": "2023-08-09" } ], "_exports": [ "as_igraph", "as_plexi_graph", "distance", "ednn", "ednn_io_prepare", "example_data", "network_gen", "p_val_count", "p_val_norm", "p_val_rank", "plexi_distance_test_isn", "plexi_distance_test1_isn", "plexi_embedding", "plexi_embedding_2layer", "plexi_node_detection_2layer", "plexi_node_distance", "Rank", "rep_random_walk", "subgraph_difference_plot", "subgraph_plot", "weightd_random_walk" ], "_help": [ { "page": "as_igraph", "title": "Convert plexi graph data to igraph", "topics": [ "as_igraph" ] }, { "page": "as_plexi_graph", "title": "Convert adjacency matrix to plexi graph data", "topics": [ "as_plexi_graph" ] }, { "page": "distance", "title": "Function to calculate distance between two vectors", "topics": [ "distance" ] }, { "page": "ednn", "title": "Encoder decoder neural network (EDNN) function", "topics": [ "ednn" ] }, { "page": "ednn_io_prepare", "title": "Preparing the input and output of the EDNN for a multiplex graph", "topics": [ "ednn_io_prepare" ] }, { "page": "example_data", "title": "Example Data", "topics": [ "example_data" ] }, { "page": "network_gen", "title": "Multiplex Network Generation", "topics": [ "network_gen" ] }, { "page": "p_val_count", "title": "Calculate p.value for x given set of null values using counts", "topics": [ "p_val_count" ] }, { "page": "p_val_norm", "title": "Calculate p.value for x given set of null values using a Gaussian null pdf", "topics": [ "p_val_norm" ] }, { "page": "p_val_rank", "title": "Calculate p.value for x given a set of null values using ranks", "topics": [ "p_val_rank" ] }, { "page": "plexi_distance_test_isn", "title": "Test the embedding distances of local neighbors change between the two conditions for ISNs.", "topics": [ "plexi_distance_test_isn" ] }, { "page": "plexi_distance_test1_isn", "title": "Test the extremeness of embedding distances of local neighbors.", "topics": [ "plexi_distance_test1_isn" ] }, { "page": "plexi_embedding", "title": "Calculate the embedding space for a multiplex network", "topics": [ "plexi_embedding" ] }, { "page": "plexi_embedding_2layer", "title": "Calculate the embedding space for a two layer multiplex network", "topics": [ "plexi_embedding_2layer" ] }, { "page": "plexi_node_detection_2layer", "title": "Detecting the nodes whose local neighbors change bweteen the two conditions.", "topics": [ "plexi_node_detection_2layer" ] }, { "page": "plexi_node_distance", "title": "Detecting the nodes whose local neighbors change between the two conditions for ISNs.", "topics": [ "plexi_node_distance" ] }, { "page": "Rank", "title": "Ranking a vector", "topics": [ "Rank" ] }, { "page": "rep_random_walk", "title": "Repetitive Fixed-length (weighted) random walk algorithm", "topics": [ "rep_random_walk" ] }, { "page": "subgraph_difference_plot", "title": "Visualization of a difference subgroup using a circular graph", "topics": [ "subgraph_difference_plot" ] }, { "page": "subgraph_plot", "title": "Visualization of a subgroup using a circular graph", "topics": [ "subgraph_plot" ] }, { "page": "weightd_random_walk", "title": "Weighted Random Walk algorithm", "topics": [ "weightd_random_walk" ] } ], "_rundeps": [ "aggregation", "assertthat", "backports", "base64enc", "cachem", "cli", "config", "cpp11", "dplyr", "farver", "fastmap", "generics", "ggforce", "ggplot2", "ggraph", "ggrepel", "glue", "graphlayouts", "gridExtra", "gtable", "here", "igraph", "isoband", "jsonlite", "keras", "labeling", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "memoise", "pillar", "pkgconfig", "png", "polyclip", "processx", "ps", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppTOML", "reticulate", "rlang", "rprojroot", "rstudioapi", "S7", "scales", "stringi", "stringr", "systemfonts", "tensorflow", "tfautograph", "tfruns", "tibble", "tidygraph", "tidyr", "tidyselect", "tweenr", "utf8", "vctrs", "viridis", "viridisLite", "whisker", "withr", "yaml", "zeallot" ], "_score": 1, "_indexed": true, "_nocasepkg": "plexi", "_universes": [ "behnam-yousefi" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.0", "date": "2026-05-27T06:57:52.000Z", "distro": "noble", "commit": "4bf3883e0614f4aa93995c96b3bab1e59c87662b", "fileid": "9a7568d062db4c0220d054400297f110dcc5d5f1d57647a8639a6d67b43c5eb0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/behnam-yousefi/actions/runs/26447429749" }, { "r": "4.6.0", "os": "linux", "version": "1.0.0", "date": "2026-05-27T06:57:51.000Z", "distro": "noble", "commit": "4bf3883e0614f4aa93995c96b3bab1e59c87662b", "fileid": "cadb36794546bfe232df7af80c57f141383d03df1fd26dd70c3f7e28509c6f33", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/behnam-yousefi/actions/runs/26447429749" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0", "date": "2026-05-27T06:58:16.000Z", "commit": "4bf3883e0614f4aa93995c96b3bab1e59c87662b", "fileid": "a8bd26cfc87949d7f10ebe39daad5a86f777f40c22ed0a089f88b99ae09b4fa6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/behnam-yousefi/actions/runs/26447429749" }, { "r": "4.6.0", "os": "mac", "version": "1.0.0", "date": "2026-05-27T06:59:27.000Z", "commit": "4bf3883e0614f4aa93995c96b3bab1e59c87662b", "fileid": "83dc6eabd9bc0f15e590589d6b25b3dfc91065606373d7d1a23c063910bf3364", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/behnam-yousefi/actions/runs/26447429749" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.0", "date": "2026-05-27T06:57:42.000Z", "commit": "4bf3883e0614f4aa93995c96b3bab1e59c87662b", "fileid": "34d581567af8c56fab197e35b69e48e5b95a90f4def93c6337c9d29af0c31bfa", "status": "success", "buildurl": "https://github.com/r-universe/behnam-yousefi/actions/runs/26447429749" }, { "r": "4.7.0", "os": "win", "version": "1.0.0", "date": "2026-05-27T06:56:47.000Z", "commit": "4bf3883e0614f4aa93995c96b3bab1e59c87662b", "fileid": "bd3e75e96a012b9cff0f7045c36dd1bf4ba8df2056f5300538bfd289ce789479", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/behnam-yousefi/actions/runs/26447429749" }, { "r": "4.5.3", "os": "win", "version": "1.0.0", "date": "2026-05-27T06:56:47.000Z", "commit": "4bf3883e0614f4aa93995c96b3bab1e59c87662b", "fileid": "aaf9070c50b64d5dd9ce6099b9f7319b59d0068b56008915478539022c43808c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/behnam-yousefi/actions/runs/26447429749" }, { "r": "4.6.0", "os": "win", "version": "1.0.0", "date": "2026-05-27T06:56:54.000Z", "commit": "4bf3883e0614f4aa93995c96b3bab1e59c87662b", "fileid": "f94c54acf94d9524f08fd11cc273d0f6003d23dba4b22bcc0ced47b82115f19a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/behnam-yousefi/actions/runs/26447429749" } ] }