{ "_id": "6a19699aacfb0bcc41de9499", "Package": "blacksheepr", "Type": "Package", "Title": "Outlier Analysis for pairwise differential comparison", "Version": "1.27.0", "Authors@R": "c(person(\"MacIntosh\", \"Cornwell\", \nemail=\"macintosh.cornwell@nyulangone.org\", \trole = c(\"aut\")),\nperson(\"RugglesLab\", email = \"ruggleslab@gmail.com\", role = \"cre\"))", "Description": "Blacksheep is a tool designed for outlier analysis in the\ncontext of pairwise comparisons in an effort to find\ndistinguishing characteristics from two groups. 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If aggregating then you will have to turn the parameter on, but you still input the outliertable. Aggregate will count the total number of outliers AND nonoutliers in its operation, so it needs the original outlier table made by the function.", "topics": [ "count_outliers" ] }, { "page": "create_heatmap", "title": "Plot out a heatmap", "topics": [ "create_heatmap" ] }, { "page": "deva", "title": "Run the entire blacksheep Function from Start to finish", "topics": [ "deva" ] }, { "page": "deva_normalization", "title": "Normalization of data to prepare for deva. Uses a Median of Ratio method followed by a log2 transformation.", "topics": [ "deva_normalization" ] }, { "page": "deva_results", "title": "Utility function that allows easier grabbing of data", "topics": [ "deva_results" ] }, { "page": "make_comparison_columns", "title": "Utility function that will take in columns with several subcategories, and output several columns each with binary classifications. ex) col1: A,B,C >> colA: A,notA,notA; colB: notB,B,notB; colC: notC,notC,C", "topics": [ "make_comparison_columns" ] }, { "page": "make_outlier_table", "title": "Separate out the \"i\"th gene, take the bounds, and then create a column that says whether or not this gene is high, low, or none in a sample with regards to the other samples in the dataset. Repeat this for every gene to create a reference table.", "topics": [ "make_outlier_table" ] }, { "page": "outlier_analysis", "title": "With the grouptablist generated by count_outliers - run through and run a fisher exact test to get the p.value for the difference in outlier count for each feature in each of your comparisons", "topics": [ "outlier_analysis" ] }, { "page": "outlier_heatmap", "title": "With the grouptablist generated by count_outliers - run through and run a fisher exact test to get the p.value for the difference in outlier count for each feature in each of your comparisons", "topics": [ "outlier_heatmap" ] }, { "page": "sample_annotationdata", "title": "sample_annotationdata", "topics": [ "sample_annotationdata" ] }, { "page": "sample_phosphodata", "title": "sample_phosphodata", "topics": [ "sample_phosphodata" ] }, { "page": "sample_rnadata", "title": "sample_rnadata", "topics": [ "sample_rnadata" ] } ], "_readme": "https://github.com/bioc/blacksheepr/raw/HEAD/README.md", "_rundeps": [ "abind", "annotate", "AnnotationDbi", "askpass", "BH", "Biobase", "BiocFileCache", "BiocGenerics", "BiocParallel", "biomaRt", "Biostrings", "bit", "bit64", "bitops", "blob", "cachem", "circlize", "cli", "clue", "cluster", "codetools", "colorspace", "ComplexHeatmap", "cpp11", "crayon", "curl", "DBI", "dbplyr", "DelayedArray", "DESeq2", "DEXSeq", "digest", "doParallel", "dplyr", "farver", "fastmap", "filelock", "foreach", "formatR", "futile.logger", "futile.options", "genefilter", "geneplotter", "generics", "GenomicRanges", "GetoptLong", "ggplot2", "GlobalOptions", "glue", "gridExtra", "gtable", "hms", "httr", "httr2", "hwriter", "IRanges", "isoband", "iterators", "jsonlite", "KEGGREST", "labeling", "lambda.r", "lattice", "lifecycle", "locfit", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "pasilla", "pillar", "pkgconfig", "png", "prettyunits", "progress", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppArmadillo", "Rhtslib", "rjson", "rlang", "Rsamtools", "RSQLite", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "shape", "snow", "SparseArray", "statmod", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridis", "viridisLite", "withr", "XML", "xml2", "xtable", "XVector" ], "_vignettes": [ { "source": "blacksheepr_vignette.Rmd", "filename": "blacksheepr_vignette.html", "title": "Outlier Analysis using blacksheepr", "author": "MacIntosh Cornwell", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Input Data", "Count data", "Annotation data", "SummarizedExperiment data", "Example Workflow - Phosphoprotein", "Read in Annotation", "Read in the phospho data", "Creating a SummarizedExperiment from our data.", "Running deva (differential extreme value analysis)", "deva parameters", "Exploring deva output", "The deva_results() function", "Results", "Piecewise analysis", "Create groupings", "Make Outlier table", "Tabulate Outliers", "Run Outlier Analysis", "Plot Results using Heatmap Generating Function", "Appendix", "Formatting your annotations table", "Using the make_comparison_columns utility function", "Running blacksheep functions for other -omics data", "Running deva with RNAseq data", "Processing data for running with deva" ], "created": "2019-10-04 21:10:31", "modified": "2019-10-11 21:56:02", "commits": 4 } ], "_score": 4.342422680822207, "_indexed": true, "_nocasepkg": "blacksheepr", "_universes": [ "bioc", "ruggleslab" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.27.0", "date": "2026-05-29T08:40:09.000Z", "distro": "noble", "commit": "3390f3ce2fcf91f6042b8a81c6b430e2eccbdae6", "fileid": "559c632a07a4c859f5b22ce45ec8cb04d76ac4f4bdb825e77f362da7b41b2a2e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626883300" }, { "r": "4.6.0", "os": "linux", "version": "1.27.0", "date": "2026-05-29T08:39:39.000Z", "distro": "noble", "commit": "3390f3ce2fcf91f6042b8a81c6b430e2eccbdae6", "fileid": "4a37680235fa940c465eb7ea9852553c16ea8e66350c2c7913003cf5ddcd8819", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626883300" }, { "r": "4.5.3", "os": "mac", "version": "1.27.0", "date": "2026-05-29T10:23:16.000Z", "commit": "3390f3ce2fcf91f6042b8a81c6b430e2eccbdae6", "fileid": "3cf90b7634fd6dbf44236d1310f2ae7c13e02187e82c61d3e4f784cb940ed520", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626883300" }, { "r": "4.6.0", "os": "mac", "version": "1.27.0", "date": "2026-05-29T10:23:20.000Z", "commit": "3390f3ce2fcf91f6042b8a81c6b430e2eccbdae6", "fileid": "89066c052611ed7b71486d8c3a46061f9b1ad27929f9d735d5a71b5297cfb6bb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626883300" }, { "r": "4.6.0", "os": "wasm", "version": "1.27.0", "date": "2026-05-29T08:39:36.000Z", "commit": "3390f3ce2fcf91f6042b8a81c6b430e2eccbdae6", "fileid": "ee5e744d721c65d8cfb20be9fb1cd0b040eec20fb3a935f52b3eac0f71393542", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626883300" }, { "r": "4.7.0", "os": "win", "version": "1.27.0", "date": "2026-05-29T08:52:49.000Z", "commit": "3390f3ce2fcf91f6042b8a81c6b430e2eccbdae6", "fileid": "9fe8a165b6fd9803b6eec5597e0c4f89c0a2000dd8a63a3541b2b293fcc8a960", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626883300" }, { "r": "4.5.3", "os": "win", "version": "1.27.0", "date": "2026-05-29T08:51:31.000Z", "commit": "3390f3ce2fcf91f6042b8a81c6b430e2eccbdae6", "fileid": "a9898ef6741663373943e5a31a957534c9ee18861563d68dcbca947baf6bb9fa", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626883300" }, { "r": "4.6.0", "os": "win", "version": "1.27.0", "date": "2026-05-29T08:54:05.000Z", "commit": "3390f3ce2fcf91f6042b8a81c6b430e2eccbdae6", "fileid": "e8767e68112a5a2524b932e3cc8e99ba330ee6c7ad5db51876530a1e810ea819", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26626883300" } ] }