{
  "_id": "6a104726acfb0bcc41c9edf3",
  "Package": "sSNAPPY",
  "Title": "Single Sample directioNAl Pathway Perturbation analYsis",
  "Version": "1.17.0",
  "Authors@R": "c(\nperson(\n\"Wenjun\", \"Liu\", , \"wenjun.liu@adelaide.edu.au\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-8185-3069\")),\nperson(\n\"Stephen\", \"Pederson\", email = \"stephen.pederson.au@gmail.com\",\nrole = \"aut\", comment = c(ORCID = \"0000-0001-8197-3303\")))",
  "Description": "A single sample pathway perturbation testing method for\nRNA-seq data. The method propagates changes in gene expression\ndown gene-set topologies to compute single-sample directional\npathway perturbation scores that reflect potential direction of\nchange. Perturbation scores can be used to test significance of\npathway perturbation at both individual-sample and treatment\nlevels.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.2.3",
  "Config/testthat/edition": "3",
  "SystemRequirements": "C++11",
  "LazyData": "false",
  "biocViews": "Software, GeneExpression, GeneSetEnrichment, GeneSignaling",
  "URL": "https://wenjun-liu.github.io/sSNAPPY/",
  "VignetteBuilder": "knitr",
  "BugReports": "https://github.com/Wenjun-Liu/sSNAPPY/issues",
  "Language": "en-US",
  "Config/pak/sysreqs": "libfontconfig1-dev libfreetype6-dev libglpk-dev\nlibicu-dev libpng-dev libxml2-dev libssl-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:58:16 UTC",
  "RemoteUrl": "https://github.com/bioc/sSNAPPY",
  "RemoteRef": "HEAD",
  "RemoteSha": "6d1ae1b5896745d0d375696f7147d9da607b0b94",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-10 09:40:00 UTC",
    "User": "root"
  },
  "Author": "Wenjun Liu [aut, cre] (ORCID: <https://orcid.org/0000-0002-8185-3069>),\nStephen Pederson [aut] (ORCID: <https://orcid.org/0000-0001-8197-3303>)",
  "Maintainer": "Wenjun Liu <wenjun.liu@adelaide.edu.au>",
  "MD5sum": "03e0fa9f52d2573e520dcbe09f6cef5d",
  "_user": "bioc",
  "_type": "src",
  "_file": "sSNAPPY_1.17.0.tar.gz",
  "_fileid": "9f97740714a1564355a54da197d6548c0c60dd6537b61a39bf54db75b22232a7",
  "_filesize": 4100027,
  "_sha256": "9f97740714a1564355a54da197d6548c0c60dd6537b61a39bf54db75b22232a7",
  "_created": "2026-05-10T09:40:00.000Z",
  "_published": "2026-05-22T12:08:06.934Z",
  "_jobs": [
    {
      "job": 77376080750,
      "time": 221,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "6902751690"
    },
    {
      "job": 77376080910,
      "time": 520,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "6902779915"
    },
    {
      "job": 77376081378,
      "time": 544,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6902781964"
    },
    {
      "job": 77376081250,
      "time": 304,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "6902850323"
    },
    {
      "job": 77376081169,
      "time": 356,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6902851581"
    },
    {
      "job": 77376080285,
      "time": 532,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6902729244"
    },
    {
      "job": 77376080368,
      "time": 183,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7160092399"
    },
    {
      "job": 77376080723,
      "time": 445,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "6902772564"
    },
    {
      "job": 77376081335,
      "time": 488,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "6902776808"
    },
    {
      "job": 77376081151,
      "time": 434,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "6902771326"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 9
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/25625264393",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/sSNAPPY",
  "_commit": {
    "id": "6d1ae1b5896745d0d375696f7147d9da607b0b94",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777381096
  },
  "_maintainer": {
    "name": "Wenjun Liu",
    "email": "wenjun.liu@adelaide.edu.au",
    "login": "wenjun-liu",
    "twitter": "@Wenjun_nora",
    "uuid": 39732084,
    "orcid": "0000-0002-8185-3069"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.3.0",
      "role": "Depends"
    },
    {
      "package": "ggplot2",
      "role": "Depends"
    },
    {
      "package": "dplyr",
      "version": ">= 1.1",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "graphite",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "ggraph",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "org.Hs.eg.db",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "edgeR",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "ggforce",
      "role": "Imports"
    },
    {
      "package": "pheatmap",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "gtools",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "BiocManager",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "colorspace",
      "role": "Suggests"
    },
    {
      "package": "cowplot",
      "role": "Suggests"
    },
    {
      "package": "DT",
      "role": "Suggests"
    },
    {
      "package": "htmltools",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "pander",
      "role": "Suggests"
    },
    {
      "package": "patchwork",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "spelling",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "tidyverse",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.17.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.16.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "geneexpression",
    "genesetenrichment",
    "genesignaling"
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "wenjun-liu",
      "count": 173,
      "uuid": 39732084
    },
    {
      "user": "smped",
      "count": 12,
      "uuid": 8252496
    },
    {
      "user": "jwokaty",
      "count": 8,
      "uuid": 1744257
    },
    {
      "user": "nturaga",
      "count": 2,
      "uuid": 2746443
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 342,
    "source": "https://www.bioconductor.org/packages/stats/bioc/sSNAPPY"
  },
  "_devurl": "https://github.com/wenjun-liu/ssnappy",
  "_pkgdown": "https://wenjun-liu.github.io/sSNAPPY/",
  "_searchresults": 21,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/sSNAPPY.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/wenjun-liu/ssnappy",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "generate_permuted_scores",
    "normalise_by_permu",
    "pathway_pert",
    "plot_community",
    "plot_gene_contribution",
    "plot_gs_network",
    "plot_gs2gene",
    "raw_gene_pert",
    "retrieve_topology",
    "weight_ss_fc"
  ],
  "_datasets": [
    {
      "name": "gsAnnotation_df",
      "title": "gsAnnotation_df: Categorization of KEGG pathways used for community annotation",
      "object": "gsAnnotation_df",
      "file": "gsAnnotation_df.rda",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "gs_name",
        "category"
      ],
      "rows": 549,
      "table": true,
      "tojson": true
    },
    {
      "name": "logCPM_example",
      "title": "logCPM_example: Normalised logCPM of patient-derived explant models obtained from 5 ER-positive primamry breast cancer tumours (GSE80098)",
      "object": "logCPM_example",
      "file": "logCPM_example.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "Vehicle_N2_48",
        "E2+R5020_N2_48",
        "R5020_N2_48",
        "Vehicle_N3_48",
        "E2+R5020_N3_48",
        "R5020_N3_48",
        "Vehicle_P4_48",
        "E2+R5020_P4_48",
        "R5020_P4_48",
        "Vehicle_P5_48",
        "E2+R5020_P5_48",
        "R5020_P5_48",
        "Vehicle_P6_48",
        "E2+R5020_P6_48",
        "R5020_P6_48"
      ],
      "rows": 7672,
      "table": true,
      "tojson": true
    },
    {
      "name": "metadata_example",
      "title": "metadata_example: Sample metadata for malignant breast cancer tumours PDE from 5 ER+ breast cancer tumour (GSE80098)",
      "object": "metadata_example",
      "file": "metadata_example.rda",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "patient",
        "treatment",
        "sample",
        "PR"
      ],
      "rows": 15,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "generate_permuted_scores",
      "title": "Permute sample labels to simulate null distribution of perturbation scores",
      "topics": [
        "generate_permuted_scores",
        "generate_permuted_scores,data.frame-method",
        "generate_permuted_scores,DGEList-method",
        "generate_permuted_scores,matrix-method",
        "generate_permuted_scores,SummarizedExperiment-method"
      ]
    },
    {
      "page": "gsAnnotation_df",
      "title": "gsAnnotation_df: Categorization of KEGG pathways used for community annotation",
      "topics": [
        "gsAnnotation_df"
      ]
    },
    {
      "page": "logCPM_example",
      "title": "logCPM_example: Normalised logCPM of patient-derived explant models obtained from 5 ER-positive primamry breast cancer tumours (GSE80098)",
      "topics": [
        "logCPM_example"
      ]
    },
    {
      "page": "metadata_example",
      "title": "metadata_example: Sample metadata for malignant breast cancer tumours PDE from 5 ER+ breast cancer tumour (GSE80098)",
      "topics": [
        "metadata_example"
      ]
    },
    {
      "page": "normalise_by_permu",
      "title": "Normalise test perturbation scores by permutation result and compute permutation p-values",
      "topics": [
        "normalise_by_permu"
      ]
    },
    {
      "page": "pathway_pert",
      "title": "Compute Single-sample Pathway-level Perturbation Score",
      "topics": [
        "pathway_pert"
      ]
    },
    {
      "page": "plot_community",
      "title": "Visualise the community structure in significantly perturbed gene-set network",
      "topics": [
        "plot_community"
      ]
    },
    {
      "page": "plot_gene_contribution",
      "title": "Plot genes' contribution to a pathway's perturbation as a heatmap",
      "topics": [
        "plot_gene_contribution"
      ]
    },
    {
      "page": "plot_gs_network",
      "title": "Plot significantly perturbed gene-sets as a network",
      "topics": [
        "plot_gs_network"
      ]
    },
    {
      "page": "plot_gs2gene",
      "title": "Plot pathways and genes contained in them as a network",
      "topics": [
        "plot_gs2gene"
      ]
    },
    {
      "page": "raw_gene_pert",
      "title": "Compute Gene-wise Perturbation Score",
      "topics": [
        "raw_gene_pert"
      ]
    },
    {
      "page": "retrieve_topology",
      "title": "Retrieve pathway topology as weighted adjacency matrices",
      "topics": [
        "retrieve_topology"
      ]
    },
    {
      "page": "sSNAPPY",
      "title": "sSNAPPY: A package for testing directional single sample pathway perturbation",
      "topics": [
        "sSNAPPY"
      ]
    },
    {
      "page": "weight_ss_fc",
      "title": "Compute weighted single sample LogFC from normalised logCPM",
      "topics": [
        "weight_ss_fc",
        "weight_ss_fc,data.frame-method",
        "weight_ss_fc,DGEList-method",
        "weight_ss_fc,matrix-method",
        "weight_ss_fc,SummarizedExperiment-method"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/sSNAPPY/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "AnnotationDbi",
    "askpass",
    "base64enc",
    "Biobase",
    "BiocGenerics",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "cachem",
    "cli",
    "cpp11",
    "crayon",
    "curl",
    "DBI",
    "DelayedArray",
    "dir.expiry",
    "dplyr",
    "edgeR",
    "farver",
    "fastmap",
    "filelock",
    "generics",
    "GenomicRanges",
    "ggforce",
    "ggplot2",
    "ggraph",
    "ggrepel",
    "glue",
    "graph",
    "graphite",
    "graphlayouts",
    "gridExtra",
    "gtable",
    "gtools",
    "httr",
    "igraph",
    "IRanges",
    "isoband",
    "jsonlite",
    "KEGGREST",
    "labeling",
    "lattice",
    "lifecycle",
    "limma",
    "locfit",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "openssl",
    "org.Hs.eg.db",
    "pheatmap",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "polyclip",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "reshape2",
    "rlang",
    "RSQLite",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "scales",
    "Seqinfo",
    "SparseArray",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "sys",
    "systemfonts",
    "tibble",
    "tidygraph",
    "tidyr",
    "tidyselect",
    "tweenr",
    "utf8",
    "vctrs",
    "viridis",
    "viridisLite",
    "withr",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "sSNAPPY.Rmd",
      "filename": "sSNAPPY.html",
      "title": "sSNAPPY: Singel Sample directioNAl Pathway Perturbation analYsis",
      "author": "Wenjun Nora Liu, Stephen Pederson",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "To get ready",
        "Installation",
        "Load packages",
        "Load data",
        "sSNAPPY workflow",
        "Compute weighted single-sample logFCs (ssLogFCs)",
        "Retrieve pathway topologies in the required format",
        "Score single sample pathway perturbation",
        "Generate null distributions of perturbation scores",
        "Test significant perturbation on",
        "single-sample level",
        "treatment-level",
        "Visualise genes' contributions to pathway perturbation",
        "Visualise overlap between gene-sets as networks",
        "Visualise community structure in the gene-set network",
        "Visualise genes included in perturbed pathways networks",
        "References",
        "Session Info"
      ],
      "created": "2022-03-28 06:18:13",
      "modified": "2023-11-01 01:55:28",
      "commits": 27
    }
  ],
  "_score": 4.799340549453582,
  "_indexed": true,
  "_nocasepkg": "ssnappy",
  "_universes": [
    "bioc",
    "wenjun-liu"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.17.0",
      "date": "2026-05-10T09:44:32.000Z",
      "distro": "noble",
      "commit": "6d1ae1b5896745d0d375696f7147d9da607b0b94",
      "fileid": "40e8e912d447b55f8b6c020863e9929d2540293c6a3e93f7b7e191b9ee61086f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25625264393"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.17.0",
      "date": "2026-05-10T09:44:38.000Z",
      "distro": "noble",
      "commit": "6d1ae1b5896745d0d375696f7147d9da607b0b94",
      "fileid": "36242c99805649c51b648f0c1dab2326469f79ca7b7c5b9ca6a0f5a8eca00ca9",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25625264393"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.17.0",
      "date": "2026-05-10T09:58:26.000Z",
      "commit": "6d1ae1b5896745d0d375696f7147d9da607b0b94",
      "fileid": "05753db89f275f77ffd3bcb954e3a9c62394df2643e8c70b735527d0066da8cf",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25625264393"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.17.0",
      "date": "2026-05-10T09:58:15.000Z",
      "commit": "6d1ae1b5896745d0d375696f7147d9da607b0b94",
      "fileid": "59f65a5e9dc202f9032cfe8a88432dc105b34bcc1cbe5f680b13cbfc9f323196",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25625264393"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.17.0",
      "date": "2026-05-10T09:42:17.000Z",
      "commit": "6d1ae1b5896745d0d375696f7147d9da607b0b94",
      "fileid": "db02545aa6c1331a093585fbfc470ae85c2a6eb2c939f233480efb3bdf717303",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25625264393"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.17.0",
      "date": "2026-05-10T09:42:50.000Z",
      "commit": "6d1ae1b5896745d0d375696f7147d9da607b0b94",
      "fileid": "c3a34ef6613b478c007b966bd5626c03df493887bdb277ea7c41a3e5fdd3cba2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25625264393"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.17.0",
      "date": "2026-05-10T09:42:09.000Z",
      "commit": "6d1ae1b5896745d0d375696f7147d9da607b0b94",
      "fileid": "4105b8bf0e9d362b7351bf5a809a21e9440360700ac2cc6820ff9818bb3fc5fc",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25625264393"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.17.0",
      "date": "2026-05-22T12:07:36.000Z",
      "commit": "6d1ae1b5896745d0d375696f7147d9da607b0b94",
      "fileid": "dfc10cd404126dcf14eb2aa17346a4703815192682b728b32ee28117b86e8f72",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/25625264393"
    }
  ]
}