From 49a12f2b830c05a1f4b7b31a1f13396f699da024 Mon Sep 17 00:00:00 2001 From: Sigve Nakken Date: Mon, 9 Sep 2024 11:43:07 +0200 Subject: [PATCH] update report DOI and CHANGELOG --- DESCRIPTION | 2 +- README.md | 6 +- docker/renv.lock | 1869 ++++++++++++++++++++++++++++++++++++--- pkgdown/index.md | 5 +- vignettes/CHANGELOG.Rmd | 16 + vignettes/running.Rmd | 2 +- 6 files changed, 1775 insertions(+), 125 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index d0ad8f8..ea54983 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -6,7 +6,7 @@ Authors@R: person(given = "Sigve", family = "Nakken", role = c("aut", "cre"), email = "sigven@ifi.uio.no", comment = c(ORCID = "0000-0001-8468-2050")) Maintainer: Sigve Nakken -URL: https://github.com/sigven/oncoEnrichR +URL: https://sigven.github.io/oncoEnrichR BugReports: https://github.com/sigven/oncoEnrichR/issues Description: oncoEnrichR performs annotation and prioritization of genesets discovered from high-throughput experiments within cancer biology. The tool diff --git a/README.md b/README.md index 9ee5002..2ae1833 100644 --- a/README.md +++ b/README.md @@ -20,14 +20,14 @@ Web-based access to **oncoEnrichR** is available at [**https://oncotools.elixir. ## News -- August 3rd 2024 [**1.5.1 release**](https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html#version-1-5-0) +- September 9th 2024 [**1.5.2 release**](https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html#version-1-5-2) +- August 3rd 2024 [**1.5.1 release**](https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html#version-1-5-1) - August 16th 2023: [**1.4.2 release**](https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html#version-1-4-2) - June 18th 2023: [**1.4.1 release**](https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html#version-1-4-1) -- February 21st 2023 [**1.4.0 release**](https://sigven.github.io/oncoEnrichR/articles/CHANGELOG.html#version-1-4-0) ## Example report -DOI +DOI ## Citation diff --git a/docker/renv.lock b/docker/renv.lock index cc0a86b..5b544b3 100644 --- a/docker/renv.lock +++ b/docker/renv.lock @@ -72,6 +72,26 @@ ], "Hash": "9bc4cabd3bfda461409172213d932813" }, + "BiocFileCache": { + "Package": "BiocFileCache", + "Version": "2.12.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", + "Requirements": [ + "DBI", + "R", + "RSQLite", + "curl", + "dbplyr", + "dplyr", + "filelock", + "httr", + "methods", + "stats", + "utils" + ], + "Hash": "9c3414bcfae204d56080dd0f0a220136" + }, "BiocGenerics": { "Package": "BiocGenerics", "Version": "0.50.0", @@ -88,11 +108,27 @@ }, "BiocManager": { "Package": "BiocManager", - "Version": "1.30.23", + "Version": "1.30.25", "Source": "Repository", "Repository": "CRAN", "Requirements": "utils", - "Hash": "47e968dfe563c1b22c2e20a067ec21d5" + "Hash": "3aec5928ca10897d7a0a1205aae64627" + }, + "BiocNeighbors": { + "Package": "BiocNeighbors", + "Version": "1.22.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", + "Requirements": [ + "BiocParallel", + "Matrix", + "Rcpp", + "RcppHNSW", + "S4Vectors", + "methods", + "stats" + ], + "Hash": "da9f332c88453734623406dcca13ee03" }, "BiocParallel": { "Package": "BiocParallel", @@ -161,14 +197,13 @@ }, "DOSE": { "Package": "DOSE", - "Version": "3.30.1", + "Version": "3.30.5", "Source": "Bioconductor", "Repository": "Bioconductor 3.19", "Requirements": [ "AnnotationDbi", "BiocParallel", "GOSemSim", - "HDO.db", "R", "fgsea", "ggplot2", @@ -176,10 +211,9 @@ "qvalue", "reshape2", "stats", - "utils", - "yulab.utils" + "utils" ], - "Hash": "befdb1b24cb92fff2499e01d4d85fb56" + "Hash": "7cb73e3595a3d1a62fc5ad013c2f280d" }, "DT": { "Package": "DT", @@ -198,6 +232,45 @@ ], "Hash": "64ff3427f559ce3f2597a4fe13255cb6" }, + "DelayedArray": { + "Package": "DelayedArray", + "Version": "0.30.1", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", + "Requirements": [ + "BiocGenerics", + "IRanges", + "Matrix", + "MatrixGenerics", + "R", + "S4Arrays", + "S4Vectors", + "SparseArray", + "methods", + "stats", + "stats4" + ], + "Hash": "395472c65cd9d606a1a345687102f299" + }, + "Deriv": { + "Package": "Deriv", + "Version": "4.1.3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": "methods", + "Hash": "bc727aba82bcda74db0bbe188ec6757c" + }, + "Formula": { + "Package": "Formula", + "Version": "1.2-5", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "stats" + ], + "Hash": "7a29697b75e027767a53fde6c903eca7" + }, "GO.db": { "Package": "GO.db", "Version": "3.19.1", @@ -211,21 +284,25 @@ }, "GOSemSim": { "Package": "GOSemSim", - 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"Hash": "94b0a21c13933f61cf6272a192964624" + "Hash": "3dc2829b790254bfba21e60965787651" }, "R6": { "Package": "R6", @@ -353,6 +583,31 @@ "Requirements": "R", "Hash": "45f0398006e83a5b10b72a90663d8d8c" }, + "RCurl": { + "Package": "RCurl", + "Version": "1.98-1.16", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "bitops", + "methods" + ], + "Hash": "ddbdf53d15b47be4407ede6914f56fbb" + }, + "RISmed": { + "Package": "RISmed", + "Version": "2.3.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "httr", + "methods", + "xml2" + ], + "Hash": "e498d442b12beb67f9785a13e5a8eb7f" + }, "RSQLite": { "Package": "RSQLite", "Version": "2.3.7", @@ -374,18 +629,18 @@ }, "Rcpp": { "Package": "Rcpp", - "Version": "1.0.12", + "Version": "1.0.13", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "methods", "utils" ], - "Hash": "5ea2700d21e038ace58269ecdbeb9ec0" + "Hash": "f27411eb6d9c3dada5edd444b8416675" }, "RcppArmadillo": { "Package": "RcppArmadillo", - "Version": "0.12.8.4.0", + "Version": "14.0.0-1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -395,11 +650,11 @@ "stats", "utils" ], - "Hash": "a535dd90aa8ec9a2e63a8f79b4a1bf43" + "Hash": "a711769be34214addf7805278b72d56b" }, "RcppEigen": { "Package": "RcppEigen", - "Version": "0.3.4.0.0", + "Version": "0.3.4.0.2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -408,7 +663,29 @@ "stats", "utils" ], - "Hash": "df49e3306f232ec28f1604e36a202847" + "Hash": "4ac8e423216b8b70cb9653d1b3f71eb9" + }, + "RcppHNSW": { + "Package": "RcppHNSW", + "Version": "0.6.0", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "Rcpp", + "methods" + ], + "Hash": "1f2dc32c27746a35196aaf95adb357be" + }, + "RcppTOML": { + "Package": "RcppTOML", + "Version": "0.2.2", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "Rcpp" + ], + "Hash": "c232938949fcd8126034419cc529333a" }, "Rhtslib": { "Package": "Rhtslib", @@ -421,9 +698,27 @@ ], "Hash": "5d6514cd44a0106581e3310f3972a82e" }, + "S4Arrays": { + "Package": "S4Arrays", + "Version": "1.4.1", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", + "Requirements": [ + "BiocGenerics", + "IRanges", + "Matrix", + "R", + "S4Vectors", + "abind", + "crayon", + "methods", + "stats" + ], + "Hash": "deeed4802c5132e88f24a432a1caf5e0" + }, "S4Vectors": { "Package": "S4Vectors", - "Version": "0.42.0", + "Version": "0.42.1", "Source": "Bioconductor", "Repository": "Bioconductor 3.19", "Requirements": [ @@ -434,11 +729,32 @@ "stats4", "utils" ], - "Hash": "245ac721ca6088200392ea5251db9e3c" + "Hash": "86398fc7c5f6be4ba29fe23ed08c2da6" + }, + "SparseArray": { + "Package": "SparseArray", + "Version": "1.4.8", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", + "Requirements": [ + "BiocGenerics", + "IRanges", + "Matrix", + "MatrixGenerics", + "R", + "S4Arrays", + "S4Vectors", + "XVector", + "matrixStats", + "methods", + "stats", + "utils" + ], + "Hash": "97f70ff11c14edd379ee2429228cbb60" }, "SparseM": { "Package": "SparseM", - "Version": "1.83", + "Version": "1.84-2", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -448,7 +764,31 @@ "stats", "utils" ], - "Hash": "f2b9f6a10ac6bc136be10c508ee890f9" + "Hash": "e78499cbcbbca98200254bd171379165" + }, + "SummarizedExperiment": { + "Package": "SummarizedExperiment", + "Version": "1.34.0", + "Source": "Bioconductor", + "Repository": "Bioconductor 3.19", + "Requirements": [ + "Biobase", + "BiocGenerics", + "DelayedArray", + "GenomeInfoDb", + "GenomicRanges", + "IRanges", + "Matrix", + "MatrixGenerics", + "R", + "S4Arrays", + "S4Vectors", + "methods", + "stats", + "tools", + "utils" + ], + "Hash": "2f6c8cc972ed6aee07c96e3dff729d15" }, "UCSC.utils": { "Package": "UCSC.utils", @@ -464,6 +804,18 @@ ], "Hash": "83d45b690bffd09d1980c224ef329f5b" }, + "XML": { + "Package": "XML", + "Version": "3.99-0.17", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "methods", + "utils" + ], + "Hash": "bc2a8a1139d8d4bd9c46086708945124" + }, "XVector": { "Package": "XVector", "Version": "0.44.0", @@ -595,6 +947,13 @@ ], "Hash": "9fe98599ca456d6552421db0d6772d8f" }, + "bitops": { + "Package": "bitops", + "Version": "1.0-8", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "da69e6b6f8feebec0827205aad3fdbd8" + }, "blob": { "Package": "blob", "Version": "1.2.4", @@ -609,7 +968,7 @@ }, "boot": { "Package": "boot", - "Version": "1.3-30", + "Version": "1.3-31", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -617,7 +976,22 @@ "graphics", "stats" ], - "Hash": "96abeed416a286d4a0f52e550b612343" + "Hash": "de2a4646c18661d6a0a08ec67f40b7ed" + }, + "brew": { + "Package": "brew", + "Version": "1.0-10", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "8f4a384e19dccd8c65356dc096847b76" + }, + "brio": { + "Package": "brio", + "Version": "1.1.5", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": "R", + "Hash": "c1ee497a6d999947c2c224ae46799b1a" }, "broom": { "Package": "broom", @@ -641,7 +1015,7 @@ }, "bslib": { "Package": "bslib", - "Version": "0.7.0", + "Version": "0.8.0", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -659,7 +1033,7 @@ "rlang", "sass" ], - "Hash": "8644cc53f43828f19133548195d7e59e" + "Hash": "b299c6741ca9746fb227debcb0f9fb6c" }, "cachem": { "Package": "cachem", @@ -672,16 +1046,29 @@ ], "Hash": "cd9a672193789068eb5a2aad65a0dedf" }, - "car": { - "Package": "car", - "Version": "3.1-2", + "callr": { + "Package": "callr", + "Version": "3.7.6", "Source": "Repository", "Repository": "CRAN", "Requirements": [ - "MASS", "R", - "abind", - "carData", + "R6", + "processx", + "utils" + ], + "Hash": "d7e13f49c19103ece9e58ad2d83a7354" + }, + "car": { + "Package": "car", + "Version": "3.1-2", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "MASS", + "R", + "abind", + "carData", "grDevices", "graphics", "lme4", @@ -704,6 +1091,49 @@ "Requirements": "R", "Hash": "ac6cdb8552c61bd36b0e54d07cf2aab7" }, + "cellranger": { + "Package": "cellranger", + "Version": "1.1.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "rematch", + "tibble" + ], + "Hash": "f61dbaec772ccd2e17705c1e872e9e7c" + }, + "checkmate": { + "Package": "checkmate", + "Version": "2.3.2", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "backports", + "utils" + ], + "Hash": "0e14e01ce07e7c88fd25de6d4260d26b" + }, + "circlize": { + "Package": "circlize", + "Version": "0.4.16", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "GlobalOptions", + "R", + "colorspace", + "grDevices", + "graphics", + "grid", + "methods", + "shape", + "stats", + "utils" + ], + "Hash": "bf366c80e2b55a5383b4af8fa2a10b74" + }, "cli": { "Package": "cli", "Version": "3.6.3", @@ -723,9 +1153,37 @@ "Requirements": "utils", "Hash": "3f038e5ac7f41d4ac41ce658c85e3042" }, + "clue": { + "Package": "clue", + "Version": "0.3-65", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "cluster", + "graphics", + "methods", + "stats" + ], + "Hash": "d6b53853800595408a776900bcc0c23f" + }, + "cluster": { + "Package": "cluster", + "Version": "2.1.6", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "grDevices", + "graphics", + "stats", + "utils" + ], + "Hash": "0aaa05204035dc43ea0004b9c76611dd" + }, "clusterProfiler": { "Package": "clusterProfiler", - 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"Version": "0.5.2", + "Version": "0.5.3", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -1917,13 +2997,13 @@ "Matrix", "R", "broom", + "doBy", "dplyr", "lme4", "methods", - "numDeriv", - "parallel" + "numDeriv" ], - "Hash": "3b5b99f4d3f067bb9c1d59317d071370" + "Hash": "938e6bbc4ac57534f8b43224506a8966" }, "pillar": { "Package": "pillar", @@ -1942,6 +3022,21 @@ ], "Hash": "15da5a8412f317beeee6175fbc76f4bb" }, + "pkgbuild": { + "Package": "pkgbuild", + "Version": "1.4.4", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "R6", + "callr", + "cli", + "desc", + "processx" + ], + "Hash": "a29e8e134a460a01e0ca67a4763c595b" + }, "pkgconfig": { "Package": "pkgconfig", "Version": "2.0.3", @@ -1950,6 +3045,58 @@ "Requirements": "utils", "Hash": "01f28d4278f15c76cddbea05899c5d6f" }, + "pkgdown": { + "Package": "pkgdown", + "Version": "2.1.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "bslib", + "callr", + "cli", + "desc", + "digest", + "downlit", + "fontawesome", + "fs", + "httr2", + "jsonlite", + "openssl", + "purrr", + "ragg", + "rlang", + "rmarkdown", + "tibble", + "whisker", + "withr", + "xml2", + "yaml" + ], + "Hash": "0d3d789055c873f48521ce7e23c23f48" + }, + "pkgload": { + "Package": "pkgload", + "Version": "1.4.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "cli", + "desc", + "fs", + "glue", + "lifecycle", + "methods", + "pkgbuild", + "processx", + "rlang", + "rprojroot", + "utils", + "withr" + ], + "Hash": "2ec30ffbeec83da57655b850cf2d3e0e" + }, "plogr": { "Package": "plogr", "Version": "0.2.0", @@ -2010,11 +3157,11 @@ }, "polyclip": { "Package": "polyclip", - 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"Hash": "dd2b9319ee0656c8acf45c7f40c59de7" + "Hash": "878b467580097e9c383acbb16adab57a" }, "purrr": { "Package": "purrr", @@ -2135,7 +3304,7 @@ }, "quarto": { "Package": "quarto", - "Version": "1.4", + "Version": "1.4.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2151,7 +3320,7 @@ "utils", "yaml" ], - "Hash": "c94c271f9b998d116186a78b2a9b23c1" + "Hash": "af456d7a181750812bd8b2bfedb3ea4e" }, "qvalue": { "Package": "qvalue", @@ -2167,6 +3336,17 @@ ], "Hash": "16f095487215acf101cdc3ed3da237cf" }, + "ragg": { + "Package": "ragg", + "Version": "1.3.2", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "systemfonts", + "textshaping" + ], + "Hash": "e3087db406e079a8a2fd87f413918ed3" + }, "rappdirs": { "Package": "rappdirs", "Version": "0.3.3", @@ -2175,6 +3355,28 @@ "Requirements": "R", "Hash": "5e3c5dc0b071b21fa128676560dbe94d" }, + "rcmdcheck": { + "Package": "rcmdcheck", + "Version": "1.4.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R6", + "callr", + "cli", + "curl", + "desc", + "digest", + "pkgbuild", + "prettyunits", + "rprojroot", + "sessioninfo", + "utils", + "withr", + "xopen" + ], + "Hash": "8f25ebe2ec38b1f2aef3b0d2ef76f6c4" + }, "readr": { "Package": "readr", "Version": "2.1.5", @@ -2198,6 +3400,61 @@ ], "Hash": "9de96463d2117f6ac49980577939dfb3" }, + "readxl": { + "Package": "readxl", + "Version": "1.4.3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "cellranger", + "cpp11", + "progress", + "tibble", + "utils" + ], + "Hash": "8cf9c239b96df1bbb133b74aef77ad0a" + }, + "registry": { + "Package": "registry", + "Version": "0.5-1", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "utils" + ], + "Hash": "1c9935f4f14c6c096c9c9072ddee59f1" + }, + "rematch": { + "Package": "rematch", + "Version": "2.0.0", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "cbff1b666c6fa6d21202f07e2318d4f1" + }, + "rematch2": { + "Package": "rematch2", + "Version": "2.1.2", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": "tibble", + "Hash": "76c9e04c712a05848ae7a23d2f170a40" + }, + "remotes": { + "Package": "remotes", + "Version": "2.5.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "methods", + "stats", + "tools", + "utils" + ], + "Hash": "3ee025083e66f18db6cf27b56e23e141" + }, "renv": { "Package": "renv", "Version": "1.0.7", @@ -2219,6 +3476,14 @@ ], "Hash": "bb5996d0bd962d214a11140d77589917" }, + "rjson": { + "Package": "rjson", + "Version": "0.2.22", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": "R", + "Hash": "ff387cabd34002e7e50d2becacb0be76" + }, "rlang": { "Package": "rlang", "Version": "1.1.4", @@ -2228,30 +3493,92 @@ "R", "utils" ], - 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"tinytex", - "tools", + "pkgload", + "purrr", + "rlang", + "stringi", + "stringr", "utils", - "xfun", - "yaml" + "withr", + "xml2" + ], + "Hash": "6ee25f9054a70f44d615300ed531ba8d" + }, + "rpart": { + "Package": "rpart", + "Version": "4.1.23", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "grDevices", + "graphics", + "stats" ], - "Hash": "27f9502e1cdbfa195f94e03b0f517484" + "Hash": "b3d390424f41d04174cccf84d49676c2" + }, + "rprojroot": { + "Package": "rprojroot", + "Version": "2.0.4", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": "R", + "Hash": "4c8415e0ec1e29f3f4f6fc108bef0144" }, "rstatix": { "Package": "rstatix", @@ -2283,6 +3610,37 @@ "Repository": "CRAN", "Hash": "96710351d642b70e8f02ddeb237c46a7" }, + "rversions": { + "Package": "rversions", + "Version": "2.1.2", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "curl", + "utils", + "xml2" + ], + "Hash": "a9881dfed103e83f9de151dc17002cd1" + }, + "rvest": { + "Package": "rvest", + "Version": "1.0.4", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "cli", + "glue", + "httr", + "lifecycle", + "magrittr", + "rlang", + "selectr", + "tibble", + "xml2" + ], + "Hash": "0bcf0c6f274e90ea314b812a6d19a519" + }, "sass": { "Package": "sass", "Version": "0.4.9", @@ -2319,7 +3677,7 @@ }, "scatterpie": { "Package": "scatterpie", - "Version": "0.2.3", + "Version": "0.2.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2331,13 +3689,40 @@ "rlang", "stats", "tidyr", + "utils", + "yulab.utils" + ], + "Hash": "cdcdfb3c27a81d3f1f12a70a8f6bfa5c" + }, + "selectr": { + "Package": "selectr", + "Version": "0.4-2", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "R6", + "methods", + "stringr" + ], + "Hash": "3838071b66e0c566d55cc26bd6e27bf4" + }, + "sessioninfo": { + "Package": "sessioninfo", + "Version": "1.2.2", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "cli", + "tools", "utils" ], - "Hash": "197ec6df5b165beb6c737ce40a8923e6" + "Hash": "3f9796a8d0a0e8c6eb49a4b029359d1f" }, "shadowtext": { "Package": "shadowtext", - "Version": "0.1.3", + "Version": "0.1.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2346,18 +3731,76 @@ "grid", "scales" ], - "Hash": "a6d0947671b22116358e2fa6595abdc4" + "Hash": "e8e4f36f4a72aff54564f730f5bc92a8" + }, + "shape": { + "Package": "shape", + "Version": "1.4.6.1", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "grDevices", + "graphics", + "stats" + ], + "Hash": "5c47e84dc0a3ca761ae1d307889e796d" + }, + "shiny": { + "Package": "shiny", + "Version": "1.9.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "R6", + "bslib", + "cachem", + "commonmark", + "crayon", + "fastmap", + "fontawesome", + "glue", + "grDevices", + "htmltools", + "httpuv", + "jsonlite", + "later", + "lifecycle", + "methods", + "mime", + "promises", + "rlang", + "sourcetools", + "tools", + "utils", + "withr", + "xtable" + ], + "Hash": "6a293995a66e12c48d13aa1f957d09c7" }, "slam": { "Package": "slam", - "Version": "0.1-50", + "Version": "0.1-53", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "R", "stats" ], - "Hash": "e25793551cbdb843154152e5ee88cbd6" + "Hash": "530404612c10533ff2deb1622c458b36" + }, + "snakecase": { + "Package": "snakecase", + "Version": "0.11.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "stringi", + "stringr" + ], + "Hash": "58767e44739b76965332e8a4fe3f91f1" }, "snow": { "Package": "snow", @@ -2370,6 +3813,29 @@ ], "Hash": "40b74690debd20c57d93d8c246b305d4" }, + "sourcetools": { + "Package": "sourcetools", + "Version": "0.1.7-1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": "R", + "Hash": "5f5a7629f956619d519205ec475fe647" + }, + "statnet.common": { + "Package": "statnet.common", + "Version": "4.9.0", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "coda", + "methods", + "parallel", + "tools", + "utils" + ], + "Hash": "be35aebf512f7b31de12200d5c3d1d67" + }, "stringi": { "Package": "stringi", "Version": "1.8.4", @@ -2416,6 +3882,18 @@ ], "Hash": "5aaa9cbaf4aba20f8e06fdea1850a398" }, + "svglite": { + "Package": "svglite", + "Version": "2.1.3", + "Source": "Repository", + "Repository": "RSPM", + "Requirements": [ + "R", + "cpp11", + "systemfonts" + ], + "Hash": "124a41fdfa23e8691cb744c762f10516" + }, "sys": { "Package": "sys", "Version": "3.4.2", @@ -2454,6 +3932,35 @@ ], "Hash": "894c8d45de6a15c2dc1a1b3832c95586" }, + "testthat": { + "Package": "testthat", + "Version": "3.2.1.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "R6", + "brio", + "callr", + "cli", + "desc", + "digest", + "evaluate", + "jsonlite", + "lifecycle", + "magrittr", + "methods", + "pkgload", + "praise", + "processx", + "ps", + "rlang", + "utils", + "waldo", + "withr" + ], + "Hash": "3f6e7e5e2220856ff865e4834766bf2b" + }, "textclean": { "Package": "textclean", "Version": "0.9.3", @@ -2488,6 +3995,19 @@ ], "Hash": "15360de1c662f65faa1c11a1d0f5bc5e" }, + "textshaping": { + "Package": "textshaping", + "Version": "0.4.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "cpp11", + "lifecycle", + "systemfonts" + ], + "Hash": "5142f8bc78ed3d819d26461b641627ce" + }, "tibble": { "Package": "tibble", "Version": "3.2.1", @@ -2591,13 +4111,24 @@ ], "Hash": "a700d295c0eff82fbce42eac067bb89d" }, + "timechange": { + "Package": "timechange", + "Version": "0.3.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "cpp11" + ], + "Hash": "c5f3c201b931cd6474d17d8700ccb1c8" + }, "tinytex": { "Package": "tinytex", - "Version": "0.51", + "Version": "0.52", "Source": "Repository", "Repository": "CRAN", "Requirements": "xfun", - "Hash": "d44e2fcd2e4e076f0aac540208559d1d" + "Hash": "cfbad971a71f0e27cec22e544a08bc3b" }, "treeio": { "Package": "treeio", @@ -2631,6 +4162,51 @@ ], "Hash": "f561504ec2897f4d46f0c7657e488ae1" }, + "urlchecker": { + "Package": "urlchecker", + "Version": "1.0.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "cli", + "curl", + "tools", + "xml2" + ], + "Hash": "409328b8e1253c8d729a7836fe7f7a16" + }, + "usethis": { + "Package": "usethis", + "Version": "3.0.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "cli", + "clipr", + "crayon", + "curl", + "desc", + "fs", + "gert", + "gh", + "glue", + "jsonlite", + "lifecycle", + "purrr", + "rappdirs", + "rlang", + "rprojroot", + "rstudioapi", + "stats", + "utils", + "whisker", + "withr", + "yaml" + ], + "Hash": "b2fbf93c2127bedd2cbe9b799530d5d2" + }, "utf8": { "Package": "utf8", "Version": "1.2.4", @@ -2641,11 +4217,11 @@ }, "uuid": { "Package": "uuid", - "Version": "1.2-0", + "Version": "1.2-1", "Source": "Repository", "Repository": "CRAN", "Requirements": "R", - "Hash": "303c19bfd970bece872f93a824e323d9" + "Hash": "34e965e62a41fcafb1ca60e9b142085b" }, "vctrs": { "Package": "vctrs", @@ -2726,9 +4302,33 @@ ], "Hash": "390f9315bc0025be03012054103d227c" }, + "waldo": { + "Package": "waldo", + "Version": "0.5.3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "cli", + "diffobj", + "glue", + "methods", + "rematch2", + "rlang", + "tibble" + ], + "Hash": "16aa934a49658677d8041df9017329b9" + }, + "whisker": { + "Package": "whisker", + "Version": "0.4.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "c6abfa47a46d281a7d5159d0a8891e88" + }, "withr": { "Package": "withr", - "Version": "3.0.0", + "Version": "3.0.1", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -2736,43 +4336,78 @@ "grDevices", "graphics" ], - "Hash": "d31b6c62c10dcf11ec530ca6b0dd5d35" + "Hash": "07909200e8bbe90426fbfeb73e1e27aa" }, "xfun": { "Package": "xfun", - "Version": "0.45", + "Version": "0.47", "Source": "Repository", "Repository": "CRAN", "Requirements": [ + "R", "grDevices", "stats", "tools" ], - "Hash": "ca59c87fe305b16a9141a5874c3a7889" + "Hash": "36ab21660e2d095fef0d83f689e0477c" + }, + "xml2": { + "Package": "xml2", + "Version": "1.3.6", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "cli", + "methods", + "rlang" + ], + "Hash": "1d0336142f4cd25d8d23cd3ba7a8fb61" + }, + "xopen": { + "Package": "xopen", + "Version": "1.0.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "processx" + ], + "Hash": "423df1e86d5533fcb73c6b02b4923b49" + }, + "xtable": { + "Package": "xtable", + "Version": "1.8-4", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "stats", + "utils" + ], + "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2" }, "yaml": { "Package": "yaml", - "Version": "2.3.8", + "Version": "2.3.10", "Source": "Repository", "Repository": "CRAN", - "Hash": "29240487a071f535f5e5d5a323b7afbd" + "Hash": "51dab85c6c98e50a18d7551e9d49f76c" }, "yulab.utils": { "Package": "yulab.utils", - "Version": "0.1.4", + "Version": "0.1.7", "Source": "Repository", "Repository": "CRAN", "Requirements": [ "cli", "digest", "fs", - "memoise", "rlang", - "stats", "tools", "utils" ], - "Hash": "60ee2aaa179dc282e9fa7367bad76e89" + "Hash": "367554cd9602e69616660580c820b3bf" }, "zip": { "Package": "zip", diff --git a/pkgdown/index.md b/pkgdown/index.md index cdfa5d8..7f660e4 100644 --- a/pkgdown/index.md +++ b/pkgdown/index.md @@ -85,11 +85,10 @@ See also the [output views](articles/output.html) that addresses each of the que ## News +- September 9th 2024: [**1.5.2 release**](articles/CHANGELOG.html#version-1-5-2) - August 3rd 2024: [**1.5.1 release**](articles/CHANGELOG.html#version-1-5-1) - August 16th 2023: [**1.4.2 release**](articles/CHANGELOG.html#version-1-4-2) - June 18th 2023: [**1.4.1 release**](articles/CHANGELOG.html#version-1-4-1) -- February 21st 2023: [**1.4.0 release**](articles/CHANGELOG.html#version-1-4-0) -- September 27th 2022: [**1.3.2 release**](articles/CHANGELOG.html#version-1-3-2) ## Citation @@ -100,7 +99,7 @@ Sigve Nakken, Sveinung Gundersen, Fabian L. M. Bernal, Dimitris Polychronopoulos ## Example report -DOI +DOI
diff --git a/vignettes/CHANGELOG.Rmd b/vignettes/CHANGELOG.Rmd index 12369de..e895fac 100644 --- a/vignettes/CHANGELOG.Rmd +++ b/vignettes/CHANGELOG.Rmd @@ -7,6 +7,22 @@ vignette: > %\usepackage[UTF-8]{inputenc} --- +## Version 1.5.2 + +* Date: 2024-09-09 + +* Updates + * Updated pre-processing code that pulls in missing pathway annotations (KEGG) + * Data updates + * KEGG - 20240904 + * WikiPathways - 20240810 (fixed bug in report display) + * MSigDB (including GO) - v2024.1.Hs + * COMPARTMENTS - 2024-09 + * BIOGRID - v4.4.237 + * Created a dedicated function `cancer_association_rank()`, which ranks a query gene + set according to strength of association (using data from the Open Targets Platform) + to a primary tumor type/site. + ## Version 1.5.1 * Date: 2024-08-03 diff --git a/vignettes/running.Rmd b/vignettes/running.Rmd index c42b0e0..0651e6b 100644 --- a/vignettes/running.Rmd +++ b/vignettes/running.Rmd @@ -103,7 +103,7 @@ A target list of *n = 134* high-confidence interacting proteins with the c-MYC o - `project_title = "cMYC_BioID_screen"` - `project_owner = "Raught et al."` -and produced the [following HTML report with results](https://doi.org/10.5281/zenodo.13170482). +and produced the [following HTML report with results](https://doi.org/10.5281/zenodo.13734871). Below are R commands provided to reproduce the example output. **NOTE**: Replace "\" with a directory on your local computer: