{ "_id": "6a1ebb09b25058d4daae0631", "Package": "POMA", "Title": "Tools for Omics Data Analysis", "Version": "1.23.0", "Authors@R": "c(person(given = \"Pol\",\nfamily = \"Castellano-Escuder\",\nrole = c(\"aut\", \"cre\"),\nemail = \"polcaes@gmail.com\",\ncomment = c(ORCID = \"0000-0001-6466-877X\"))\n)", "Description": "The POMA package offers a comprehensive toolkit designed\nfor omics data analysis, streamlining the process from initial\nvisualization to final statistical analysis. Its primary goal\nis to simplify and unify the various steps involved in omics\ndata processing, making it more accessible and manageable\nwithin a single, intuitive R package. Emphasizing on\nreproducibility and user-friendliness, POMA leverages the\nstandardized SummarizedExperiment class from Bioconductor,\nensuring seamless integration and compatibility with a wide\narray of Bioconductor tools. This approach guarantees maximum\nflexibility and replicability, making POMA an essential asset\nfor researchers handling omics datasets. See\nhttps://github.com/pcastellanoescuder/POMAShiny. Paper:\nCastellano-Escuder et al. (2021)\n for more details.", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "biocViews": "BatchEffect, Classification, Clustering, DecisionTree,\nDimensionReduction, MultidimensionalScaling, Normalization,\nPreprocessing, PrincipalComponent, Regression, RNASeq,\nSoftware, StatisticalMethod, Visualization", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "URL": "https://github.com/pcastellanoescuder/POMA", "BugReports": "https://github.com/pcastellanoescuder/POMA/issues", "Config/pak/sysreqs": "cmake libfreetype6-dev libglpk-dev libglu1-mesa-dev\nlibgmp3-dev make texlive libicu-dev libpng-dev libuv1-dev\nlibxml2-dev libmpfr-dev libgl1-mesa-dev libssl-dev perl\nzlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:53:17 UTC", "RemoteUrl": "https://github.com/bioc/POMA", "RemoteRef": "HEAD", "RemoteSha": "abb075a6ecc710996b5c8e77ce475c92b3f2c241", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-02 11:04:02 UTC", "User": "root" }, "Author": "Pol Castellano-Escuder [aut, cre] (ORCID:\n)", "Maintainer": "Pol Castellano-Escuder ", "MD5sum": "a33a411901df2bb9a155db10cb9ef918", "_user": "bioc", "_type": "src", "_file": "POMA_1.23.0.tar.gz", "_fileid": "39c5145010efdd867aeeea20655c9b36a9182a3b3c24f05c5e29592bd249db8e", "_filesize": 1962510, "_sha256": "39c5145010efdd867aeeea20655c9b36a9182a3b3c24f05c5e29592bd249db8e", "_created": "2026-06-02T11:04:02.000Z", "_published": "2026-06-02T11:14:17.847Z", "_jobs": [ { "job": 79056478543, "time": 272, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7356022666" }, { "job": 79056478524, "time": 506, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7356100100" }, { "job": 79056478612, "time": 505, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7356099964" }, { "job": 79056478539, "time": 262, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7356116964" }, { "job": 79056478555, "time": 287, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7356120072" }, { "job": 79055526685, "time": 351, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7355935704" }, { "job": 79056478530, "time": 235, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7356010780" }, { "job": 79056478622, "time": 285, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7356027054" }, { "job": 79056478535, "time": 342, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7356044551" }, { "job": 79056478701, "time": 353, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7356048417" } ], "_bioccheck": { "error": 1, "warning": 1, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26815302533", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/POMA", "_commit": { "id": "abb075a6ecc710996b5c8e77ce475c92b3f2c241", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380797 }, "_maintainer": { "name": "Pol Castellano-Escuder", "email": "polcaes@gmail.com", "login": "pcastellanoescuder", "linkedin": "in/polcastellanoescuder", "twitter": "@polcastellano_", "description": "Co-Founder & CTO \n@heurekalabsco", "uuid": 38317483, "orcid": "0000-0001-6466-877X" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "broom", "role": "Imports" }, { "package": "caret", "role": "Imports" }, { "package": "ComplexHeatmap", "role": "Imports" }, { "package": "dbscan", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "DESeq2", "role": "Imports" }, { "package": "fgsea", "role": "Imports" }, { "package": "FSA", "role": "Imports" }, { "package": "ggcorrplot", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "ggrepel", "role": "Imports" }, { "package": "glmnet", "role": "Imports" }, { "package": "grid", "role": "Imports" }, { "package": "impute", "role": "Imports" }, { "package": "janitor", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "lme4", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "mixOmics", "role": "Imports" }, { "package": "multcomp", "role": "Imports" }, { "package": "msigdbr", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "randomForest", "role": "Imports" }, { "package": "RankProd", "version": ">= 3.14", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "sva", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "uwot", "role": "Imports" }, { "package": "vegan", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "covr", "role": "Suggests" }, { "package": "ggraph", "role": "Suggests" }, { "package": "ggtext", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "patchwork", "role": "Suggests" }, { "package": "plotly", "role": "Suggests" }, { "package": "tidyverse", "role": "Suggests" }, { "package": "testthat", "version": ">= 2.3.2", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.23.0", "bioc": "3.24" }, { "branch": "release", "version": "1.22.0", "bioc": "3.23" } ], "_topics": [ "batcheffect", "classification", "clustering", "decisiontree", "dimensionreduction", "multidimensionalscaling", "normalization", "preprocessing", "principalcomponent", "regression", "rnaseq", "software", "statisticalmethod", "visualization", "bioconductor", "bioinformatics", "data-visualization", "dimension-reduction", "exploratory-data-analysis", "machine-learning", "omics-data-integration", "pipeline", "pre-processing", "statistical-analysis", "user-friendly", "workflow" ], "_stars": 14, "_contributors": [ { "user": "pcastellanoescuder", "count": 304, "uuid": 38317483 }, { "user": "jwokaty", "count": 10, "uuid": 1744257 }, { "user": "nturaga", "count": 8, "uuid": 2746443 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 428, "source": "https://www.bioconductor.org/packages/stats/bioc/POMA" }, "_mentions": 20, "_devurl": "https://github.com/pcastellanoescuder/poma", "_searchresults": 48, "_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/POMA.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/pcastellanoescuder/poma", "_realowner": "bioc", "_cranurl": false, "_exports": [ "%>%", "poma_pal_c", "poma_pal_d", "PomaBatch", "PomaBoxplots", "PomaClust", "PomaCorr", "PomaCreateObject", "PomaDensity", "PomaDESeq", "PomaEnrichment", "PomaHeatmap", "PomaImpute", "PomaLasso", "PomaLimma", "PomaLM", "PomaLMM", "PomaNorm", "PomaOddsRatio", "PomaOutliers", "PomaPCA", "PomaPCR", "PomaPLS", "PomaRandForest", "PomaRankProd", "PomaUMAP", "PomaUnivariate", "PomaVolcano", "scale_color_poma_c", "scale_color_poma_d", "scale_fill_poma_c", "scale_fill_poma_d", "theme_poma" ], "_datasets": [ { "name": "st000284", "title": "Colorectal Cancer Detection Using Targeted Serum Metabolic Profiling", "object": "st000284", "class": [ "SummarizedExperiment" ], "fields": [], "table": false, "tojson": false }, { "name": "st000336", "title": "Targeted LC/MS of urine from boys with DMD and controls", "object": "st000336", "class": [ "SummarizedExperiment" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "box_cox_transformation", "title": "Box-Cox Transformation", "topics": [ "box_cox_transformation" ] }, { "page": "cor_pmat", "title": "Correlation P-Values", "topics": [ "cor_pmat" ] }, { "page": "detect_decimals", "title": "Detect decimals", "topics": [ "detect_decimals" ] }, { "page": "flattenCorrMatrix", "title": "Flatten Correlation Matrix", "topics": [ "flattenCorrMatrix" ] }, { "page": "poma_pal_c", "title": "Return function to interpolate a continuous POMA color palette", "topics": [ "poma_pal_c" ] }, { "page": "poma_pal_d", "title": "Return function to interpolate a discrete POMA color palette", "topics": [ "poma_pal_d" ] }, { "page": "PomaBatch", "title": "Batch Correction", "topics": [ "PomaBatch" ] }, { "page": "PomaBoxplots", "title": "Boxplots and Violin Plots", "topics": [ "PomaBoxplots" ] }, { "page": "PomaClust", "title": "Cluster Analysis", "topics": [ "PomaClust" ] }, { "page": "PomaCorr", "title": "Correlation Analysis", "topics": [ "PomaCorr" ] }, { "page": "PomaCreateObject", "title": "Create a 'SummarizedExperiment' Object", "topics": [ "PomaCreateObject" ] }, { "page": "PomaDensity", "title": "Density Plots", "topics": [ "PomaDensity" ] }, { "page": "PomaDESeq", "title": "Differential Expression Analysis Based on the Negative Binomial Distribution", "topics": [ "PomaDESeq" ] }, { "page": "PomaEnrichment", "title": "Enrichment Analysis", "topics": [ "PomaEnrichment" ] }, { "page": "PomaHeatmap", "title": "Heatmap Plot", "topics": [ "PomaHeatmap" ] }, { "page": "PomaImpute", "title": "Impute Missing Values", "topics": [ "PomaImpute" ] }, { "page": "PomaLasso", "title": "Lasso, Ridge, and Elasticnet Regularized Generalized Linear Models for Binary Outcomes", "topics": [ "PomaLasso" ] }, { "page": "PomaLimma", "title": "Differential Expression Analysis Using 'limma'", "topics": [ "PomaLimma" ] }, { "page": "PomaLM", "title": "Linear Models", "topics": [ "PomaLM" ] }, { "page": "PomaLMM", "title": "Linear Mixed Models", "topics": [ "PomaLMM" ] }, { "page": "PomaNorm", "title": "Normalize Data", "topics": [ "PomaNorm" ] }, { "page": "PomaOddsRatio", "title": "Logistic Regression Model Odds Ratios", "topics": [ "PomaOddsRatio" ] }, { "page": "PomaOutliers", "title": "Analyse and Remove Statistical Outliers", "topics": [ "PomaOutliers" ] }, { "page": "PomaPCA", "title": "Principal Components Analysis", "topics": [ "PomaPCA" ] }, { "page": "PomaPCR", "title": "Principal Components Regression", "topics": [ "PomaPCR" ] }, { "page": "PomaPLS", "title": "Partial Least Squares Methods", "topics": [ "PomaPLS" ] }, { "page": "PomaRandForest", "title": "Classification Random Forest", "topics": [ "PomaRandForest" ] }, { "page": "PomaRankProd", "title": "Rank Product/Rank Sum Analysis", "topics": [ "PomaRankProd" ] }, { "page": "PomaUMAP", "title": "Dimensionality Reduction with UMAP", "topics": [ "PomaUMAP" ] }, { "page": "PomaUnivariate", "title": "Univariate Statistical Test", "topics": [ "PomaUnivariate" ] }, { "page": "PomaVolcano", "title": "Volcano Plot", "topics": [ "PomaVolcano" ] }, { "page": "quantile_norm", "title": "Sample Quantile Normalization", "topics": [ "quantile_norm" ] }, { "page": "scale_color_poma_c", "title": "Color scale constructor for continuous 'viridis' \"plasma\" palette", "topics": [ "scale_color_poma_c" ] }, { "page": "scale_color_poma_d", "title": "Color scale constructor for discrete 'viridis' \"plasma\" palette", "topics": [ "scale_color_poma_d" ] }, { "page": "scale_fill_poma_c", "title": "Fill scale constructor for continuous 'viridis' \"plasma\" palette", "topics": [ "scale_fill_poma_c" ] }, { "page": "scale_fill_poma_d", "title": "Fill scale constructor for discrete 'viridis' \"plasma\" palette", "topics": [ "scale_fill_poma_d" ] }, { "page": "st000284", "title": "Colorectal Cancer Detection Using Targeted Serum Metabolic Profiling", "topics": [ "st000284" ] }, { "page": "st000336", "title": "Targeted LC/MS of urine from boys with DMD and controls", "topics": [ "st000336" ] }, { "page": "sum_norm", "title": "Sample Sum Normalization", "topics": [ "sum_norm" ] }, { "page": "theme_poma", "title": "A ggplot theme which allow custom yet consistent styling of plots in the POMA package and web app.", "topics": [ "theme_poma" ] } ], "_pkglogo": "https://github.com/bioc/POMA/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/bioc/POMA/raw/HEAD/README.md", "_rundeps": [ "abind", "annotate", "AnnotationDbi", "askpass", "assertthat", "babelgene", "backports", "base64enc", "BH", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "bit", "bit64", "blob", "boot", "broom", "bslib", "ca", "cachem", "car", "carData", "caret", "circlize", "class", "cli", "clock", "clue", "cluster", "codetools", "colorspace", "ComplexHeatmap", "corpcor", "corrr", "cowplot", "cpp11", "crayon", "curl", "data.table", "DBI", "dbscan", "DelayedArray", "Deriv", "DESeq2", "diagram", "digest", "doBy", "doParallel", "dplyr", "dqrng", "dunn.test", "e1071", "edgeR", "ellipse", "evaluate", "farver", "fastmap", "fastmatch", "fgsea", "FlexParamCurve", "FNN", "fontawesome", "foreach", "forecast", "formatR", "Formula", "fracdiff", "fs", "FSA", "futile.logger", "futile.options", "future", "future.apply", "gclus", "genefilter", "generics", "GenomicRanges", "GetoptLong", "ggcorrplot", "ggplot2", "ggrepel", "glmnet", "GlobalOptions", "globals", "glue", "gmp", "gower", "gridExtra", "gtable", "hardhat", "highr", "hms", "htmltools", "htmlwidgets", "httr", "igraph", "impute", "ipred", "IRanges", "irlba", "isoband", "iterators", "janitor", "jquerylib", "jsonlite", "KEGGREST", "KernSmooth", "knitr", "labeling", "lambda.r", "lattice", "lava", "lifecycle", "limma", "listenv", "lme4", "lmtest", "locfit", "lubridate", "magrittr", "MASS", "Matrix", "MatrixGenerics", "MatrixModels", "matrixStats", "memoise", "mgcv", "microbenchmark", "mime", "minqa", "mixOmics", "ModelMetrics", "modelr", "msigdbr", "multcomp", "mvtnorm", "nlme", "nloptr", "nnet", "numDeriv", "openssl", "parallelly", "pbkrtest", "permute", "pillar", "pkgconfig", "plotrix", "plyr", "png", "pROC", "prodlim", "progressr", "proxy", "purrr", "qap", "quantreg", "R6", "randomForest", "RankProd", "rappdirs", "rARPACK", "rbibutils", "RColorBrewer", "Rcpp", "RcppAnnoy", "RcppArmadillo", "RcppEigen", "RcppProgress", "Rdpack", "recipes", "reformulas", "registry", "reshape2", "rgl", "rjson", "rlang", "rmarkdown", "Rmpfr", "rpart", "RSpectra", "RSQLite", "S4Arrays", "S4Vectors", "S7", "sandwich", "sass", "scales", "scrutiny", "Seqinfo", "seriation", "shape", "sitmo", "snakecase", "snow", "SparseArray", "SparseM", "sparsevctrs", "SQUAREM", "statmod", "stringi", "stringr", "SummarizedExperiment", "survival", "sva", "sys", "TH.data", "tibble", "tidyr", "tidyselect", "timechange", "timeDate", "tinytex", "TSP", "tzdb", "urca", "utf8", "uwot", "vctrs", "vegan", "viridisLite", "withr", "xfun", "XML", "xtable", "XVector", "yaml", "zoo" ], "_vignettes": [ { "source": "POMA-workflow.Rmd", "filename": "POMA-workflow.html", "title": "Get Started", "author": "Pol Castellano-Escuder, Ph.D.", "engine": "knitr::rmarkdown", "headings": [ "Installation", "Load POMA", "The POMA Workflow", "Data Preparation", "Pre Processing", "Missing Value Imputation", "Normalization", "Normalization effect", "Outlier Detection", "Session Information", "References" ], "created": "2023-12-08 15:48:06", "modified": "2024-01-21 23:44:23", "commits": 5 }, { "source": "POMA-normalization.Rmd", "filename": "POMA-normalization.html", "title": "Normalization Methods", "author": "Pol Castellano-Escuder, Ph.D.", "engine": "knitr::rmarkdown", "headings": [ "Installation", "Load Packages", "Load Data and Imputation", "Normalization", "Normalization effect on data dimensions", "Normalization effect on samples", "Normalization effect on features", "Session Information", "References" ], "created": "2020-02-09 05:45:54", "modified": "2024-08-20 17:21:21", "commits": 19 } ], "_score": 7.906550519101451, "_indexed": true, "_nocasepkg": "poma", "_universes": [ "bioc", "pcastellanoescuder" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.23.0", "date": "2026-06-02T11:08:53.000Z", "distro": "noble", "commit": "abb075a6ecc710996b5c8e77ce475c92b3f2c241", "fileid": "1b819ffdc722e1a28855c81ac66e56f04f114d284a23f6d8197440999665039a", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26815302533" }, { "r": "4.6.0", "os": "linux", "version": "1.23.0", "date": "2026-06-02T11:08:44.000Z", "distro": "noble", "commit": "abb075a6ecc710996b5c8e77ce475c92b3f2c241", "fileid": "595dcf93afeaa2b7621d0a7f7e0e38374c30f9aaa0c0acf74a89f5fa4e927b54", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26815302533" }, { "r": "4.5.3", "os": "mac", "version": "1.23.0", "date": "2026-06-02T11:10:55.000Z", "commit": "abb075a6ecc710996b5c8e77ce475c92b3f2c241", "fileid": "07f49628f369b5adb5b0186a3f7224e16c59f6a6ed3d56099a51d01c218891f7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26815302533" }, { "r": "4.6.0", "os": "mac", "version": "1.23.0", "date": "2026-06-02T11:10:47.000Z", "commit": "abb075a6ecc710996b5c8e77ce475c92b3f2c241", "fileid": "c55dafe7eee4d0d443be669051920e77bd0059f423cd3bbf52eed304668a540f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26815302533" }, { "r": "4.6.0", "os": "wasm", "version": "1.23.0", "date": "2026-06-02T11:08:19.000Z", "commit": "abb075a6ecc710996b5c8e77ce475c92b3f2c241", "fileid": "4823ee77a310c5fdadffa834704b0144bb5ffb708ed0e11f55e0b853e22a0f4b", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26815302533" }, { "r": "4.7.0", "os": "win", "version": "1.23.0", "date": "2026-06-02T11:06:16.000Z", "commit": "abb075a6ecc710996b5c8e77ce475c92b3f2c241", "fileid": "79b81d04e154133550a42d20ef1d174adc931f8b1092670cc7034725283d5604", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26815302533" }, { "r": "4.5.3", "os": "win", "version": "1.23.0", "date": "2026-06-02T11:05:47.000Z", "commit": "abb075a6ecc710996b5c8e77ce475c92b3f2c241", "fileid": "a6134e4aa4a1da9401524368c651c339c78218700c12988a810b30e4fd57699f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26815302533" }, { "r": "4.6.0", "os": "win", "version": "1.23.0", "date": "2026-06-02T11:06:08.000Z", "commit": "abb075a6ecc710996b5c8e77ce475c92b3f2c241", "fileid": "ade8b79c1bacb353f74820ff631e92d50801174ea3ec258c6ed4c30573953809", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26815302533" } ] }