{ "_id": "6a1972efacfb0bcc41def089", "Package": "autonomics", "Type": "Package", "Title": "Unified Statistical Modeling of Omics Data", "Version": "1.21.0", "Authors@R": "c(person('Aditya', 'Bhagwat', email = 'aditya.bhagwat@uni-marburg.de', role = c('aut', 'cre')), \nperson('Richard', 'Cotton', email = 'richierocks@gmail.com', role = c('aut')),\nperson('Vanessa', 'Beutgen', email = 'vanessa.beutgen@uni-marburg.de', role = c('ctb')),\nperson('Witold', 'Szymanski', email = 'witold.szymanski@uni-marburg.de', role = c('ctb')),\nperson('Shahina', 'Hayat', email = 'shahina.hayat@hotmail.com', role = c('ctb')),\nperson('Laure', 'Cougnaud', email = 'laure.cougnaud@openanalytics.eu', role = c('ctb')),\nperson('Hinrich', 'Goehlmann', email = 'hinrich@goehlmann.info', role = c('sad')),\nperson('Karsten', 'Suhre', email = 'kas2049@qatar-med.cornell.edu', role = c('sad')),\nperson('Johannes', 'Graumann', email = 'johannes.graumann@uni-marburg.de', role = c('aut', 'sad'))\n)", "Description": "This package unifies access to Statistal Modeling of Omics\nData. 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".read_diann_proteingroups", "read_diann", "read_diann_proteingroups" ] }, { "page": "dot-read_maxquant_proteingroups", "title": "Read proteingroups/phosphosites as-is", "topics": [ ".read_maxquant_phosphosites", ".read_maxquant_proteingroups" ] }, { "page": "read_metabolon", "title": "Read metabolon xlsxfile", "topics": [ ".read_metabolon", "read_metabolon" ] }, { "page": "read_rectangles", "title": "Read omics data from rectangular file", "topics": [ ".read_rectangles", "read_rectangles" ] }, { "page": "read_rnaseq_counts", "title": "Read rnaseq counts/bams", "topics": [ ".read_rnaseq_bams", ".read_rnaseq_counts", "read_rnaseq_bams", "read_rnaseq_counts" ] }, { "page": "read_somascan", "title": "Read somascan adatfile", "topics": [ ".read_somascan", "read_somascan" ] }, { "page": "abstract_fit", "title": "Abstract model fit", "topics": [ "abstract_fit" ] }, { "page": "add_adjusted_pvalues", "title": "Add adjusted pvalues", "topics": [ "add_adjusted_pvalues", "add_adjusted_pvalues.data.table", "add_adjusted_pvalues.NULL", "add_adjusted_pvalues.SummarizedExperiment" ] }, { "page": "add_assay_means", "title": "Add assay means", "topics": [ "add_assay_means" ] }, { "page": "add_facetvars", "title": "Add facetvars", "topics": [ "add_facetvars" ] }, { "page": "add_opentargets_by_uniprot", "title": "Add opentargets annotations", "topics": [ "add_opentargets_by_uniprot" ] }, { "page": "add_psp", "title": "Add psp", "topics": [ "add_psp" ] }, { "page": "add_smiles", "title": "Add smiles", "topics": [ "add_smiles" ] }, { "page": "altenrich", "title": "Alternative Enrichment Analysis", "topics": [ "altenrich" ] }, { "page": "analysis", "title": "Get/set analysis", "topics": [ "analysis", "analysis,SummarizedExperiment-method", "analysis<-", "analysis<-,SummarizedExperiment,list-method" ] }, { "page": "analyze", "title": "Analyze", "topics": [ "analyze" ] }, { "page": "annotate_compounddiscoverer", "title": "Read compound discoverer output", "topics": [ "annotate_compounddiscoverer" ] }, { "page": "annotate_maxquant", "title": "Annotate maxquant", "topics": [ "annotate_maxquant" ] }, { "page": "annotate_uniprot_rest", "title": "Annotate uniprot/ensp", "topics": [ "annotate_uniprot_rest" ] }, { "page": "assert_is_valid_sumexp", "title": "Assert that x is a valid SummarizedExperiment", "topics": [ "assert_is_valid_sumexp" ] }, { "page": "AUTONOMICS_DATASETS", "title": "Data used in examples/vignette/tests/longtests", "topics": [ "AUTONOMICS_DATASETS" ] }, { "page": "awblinmod", "title": "General Linear Modeling (across-within-between interface)", "topics": [ "awblinmod", "awblinmod_limma", "awblinmod_lm", "awblinmod_lme", "awblinmod_lmer" ] }, { "page": "biplot", "title": "Biplot", "topics": [ "biplot" ] }, { "page": "biplot_corrections", "title": "Biplot batch corrections", "topics": [ "biplot_corrections" ] }, { "page": "biplot_covariates", "title": "Biplot covariates", "topics": [ "biplot_covariates" ] }, { "page": "block_has_two_levels", "title": "Block has two levels", "topics": [ "block_has_two_levels" ] }, { "page": "block2limma", "title": "block2limma", "topics": [ "block2limma", "block2limma.character", "block2limma.formula", "block2limma.list", "block2limma.NULL" ] }, { "page": "block2lm", "title": "block2lm", "topics": [ "block2lm", "block2lm.character", "block2lm.formula", "block2lm.list", "block2lm.NULL" ] }, { "page": "block2lme", "title": "block2lme", "topics": [ "block2lme", "block2lme.character", "block2lme.formula", "block2lme.list" ] }, { "page": "block2lmer", "title": "block2lmer", "topics": [ "block2lmer", "block2lmer.character", "block2lmer.formula", "block2lmer.list" ] }, { "page": "center", "title": "Center samples", "topics": [ "center", "center_mean", "center_median" ] }, { "page": "code", "title": "Contrast Code Factor", "topics": [ "code", "code.character", "code.data.table", "code.factor", "code.logical", "code.numeric", "code_control", "code_deviation", "code_deviation_first", "code_diff", "code_diff_forward", "code_helmert", "code_helmert_forward", "contr.diff", "contr.treatment.explicit" ] }, { "page": "collapsed_entrezg_to_symbol", "title": "Collapsed entrezg to genesymbol", "topics": [ "collapsed_entrezg_to_symbol" ] }, { "page": "COMPOUNDDISCOVERER_PATTERNS", "title": "compound discoverer quantity patterns", "topics": [ "COMPOUNDDISCOVERER_PATTERNS" ] }, { "page": "model_coefs", "title": "Get model coefs", "topics": [ "contrast_coefs", "model_coefs" ] }, { "page": "contrast_subgroup_cols", "title": "Row/Col contrasts", "topics": [ "contrast_subgroup_cols", "contrast_subgroup_rows" ] }, { "page": "contrastdt", "title": "Get contrastdt", "topics": [ "contrastdt" ] }, { "page": "count_in", "title": "Count/Collapse in/outside intersection", "topics": [ "collapse_in", "collapse_in.character", "collapse_in.factor", "collapse_in.list", "count_in", "count_in.character", "count_in.factor", "count_in.list", "count_out", "count_out.character", "count_out.factor", "count_out.list" ] }, { "page": "counts", "title": "Get/Set counts", "topics": [ "counts", "counts,SummarizedExperiment-method", "counts<-", "counts<-,SummarizedExperiment,matrix-method", "counts<-,SummarizedExperiment,NULL-method", "counts<-,SummarizedExperiment,numeric-method" ] }, { "page": "counts2cpm", "title": "Convert between counts and cpm/tpm", "topics": [ "counts2cpm", "cpm2counts" ] }, { "page": "counts2tpm", "title": "counts to tpm", "topics": [ "counts2tpm" ] }, { "page": "cpm", "title": "Get/Set cpm", "topics": [ "cpm", "cpm,SummarizedExperiment-method", "cpm<-", "cpm<-,SummarizedExperiment,matrix-method", "cpm<-,SummarizedExperiment,numeric-method" ] }, { "page": "create_design", "title": "Create design matrix", "topics": [ "create_design", "create_design.data.table", "create_design.SummarizedExperiment" ] }, { "page": "download_data", "title": "Download autonomics example data", "topics": [ "DATADIR", "download_data" ] }, { "page": "default_formula", "title": "Create default formula", "topics": [ "default_formula" ] }, { "page": "default_geom", "title": "Default geom", "topics": [ "default_geom" ] }, { "page": "default_sfile", "title": "Default sfile", "topics": [ "default_sfile" ] }, { "page": "defaultmsigfile", "title": "Default msigdb file", "topics": [ "defaultmsigfile" ] }, { "page": "demultiplex", "title": "Demultiplex snames", "topics": [ "demultiplex" ] }, { "page": "dequantify", "title": "Dequantify maxquant snames", "topics": [ "dequantify" ] }, { "page": "dequantify_compounddiscoverer", "title": "dequantify_compounddiscoverer compound discoverer snames", "topics": [ "dequantify_compounddiscoverer" ] }, { "page": "DIMREDENGINES", "title": "Dimension Reduction Methods", "topics": [ "DIMREDENGINES", "DIMREDSUPER", "DIMREDUN" ] }, { "page": "download_gtf", "title": "Download GTF file", "topics": [ "download_gtf" ] }, { "page": "download_mcclain21", "title": "Download mcclain21 data", "topics": [ "download_mcclain21" ] }, { "page": "dt2mat", "title": "`data.table` to `matrix`", "topics": [ "dt2mat", "mat2dt" ] }, { "page": "enrichment", "title": "Enrichment analysis", "topics": [ "enrichment" ] }, { "page": "taxon2org", "title": "taxon/ens to organism", "topics": [ "ens2org", "taxon2org" ] }, { "page": "entrezg_to_symbol", "title": "Entrezg to genesymbol", "topics": [ "entrezg_to_symbol" ] }, { "page": "extract_rectangle", "title": "Extract rectangle from omics file, data.table, or matrix", "topics": [ "extract_rectangle", "extract_rectangle.character", "extract_rectangle.data.table", "extract_rectangle.matrix" ] }, { "page": "factorize", "title": "Factorize/Bin", "topics": [ "bin", "bin.character", "bin.factor", "bin.logical", "bin.matrix", "bin.numeric", "bin.SummarizedExperiment", "bin_assay", "factorize", "factorize.character", "factorize.factor", "factorize.logical", "factorize.matrix", "factorize.numeric", "factorize.SummarizedExperiment", "factorize_assay" ] }, { "page": "fcluster", "title": "Cluster features", "topics": [ "fcluster" ] }, { "page": "fdata", "title": "Get/Set sample/feature data", "topics": [ "fdata", "fdata,SummarizedExperiment-method", "fdata<-", "fdata<-,SummarizedExperiment,data.frame-method", "fdt", "fdt,SummarizedExperiment-method", "fdt<-", "fdt<-,SummarizedExperiment,data.table-method", "sdata", "sdata,SummarizedExperiment-method", "sdata<-", "sdata<-,SummarizedExperiment,data.frame-method", "sdata<-,SummarizedExperiment,DataFrame-method", "sdt", "sdt,SummarizedExperiment-method", "sdt<-", "sdt<-,SummarizedExperiment,data.table-method" ] }, { "page": "fdr2p", "title": "fdr to p", "topics": [ "fdr2p" ] }, { "page": "filter_exprs_replicated_in_some_subgroup", "title": "Filter features with replicated expression in some subgroup", "topics": [ "filter_exprs_replicated_in_some_subgroup" ] }, { "page": "filter_features", "title": "Filter features on condition", "topics": [ "filter_features" ] }, { "page": "filter_medoid", "title": "Filter medoid sample", "topics": [ "filter_medoid" ] }, { "page": "filter_samples", "title": "Filter samples on condition", "topics": [ "filter_samples" ] }, { "page": "fits", "title": "Get fit models", "topics": [ "coefs", "coefs.data.table", "coefs.factor", "coefs.NULL", "coefs.SummarizedExperiment", "fitcoefs", "fits", "fits.data.table", "fits.NULL", "fits.SummarizedExperiment" ] }, { "page": "fix_xlgenes", "title": "Fix excel genes", "topics": [ "fix_xlgenes" ] }, { "page": "flevels", "title": "Get fvar levels", "topics": [ "flevels" ] }, { "page": "fnames", "title": "Get/Set fnames", "topics": [ "fnames", "fnames,SummarizedExperiment-method", "fnames<-", "fnames<-,SummarizedExperiment,character-method" ] }, { "page": "formula2str", "title": "formula to string", "topics": [ "formula2str" ] }, { "page": "ftype", "title": "Feature type", "topics": [ "ftype" ] }, { "page": "fvalues", "title": "Get fvalues", "topics": [ "fvalues" ] }, { "page": "fvars", "title": "Get/Set fvars", "topics": [ "fvars", "fvars,SummarizedExperiment-method", "fvars<-", "fvars<-,SummarizedExperiment,character-method" ] }, { "page": "genome_to_orgdb", "title": "Get corresponding orgdb", "topics": [ "genome_to_orgdb" ] }, { "page": "group_by_level", "title": "group by level", "topics": [ "group_by_level", "group_by_level.character", "group_by_level.data.table", "group_by_level.factor" ] }, { "page": "guess_compounddiscoverer_quantity", "title": "Guess compound discoverer quantity from snames", "topics": [ "guess_compounddiscoverer_quantity" ] }, { "page": "guess_fitsep", "title": "guess fitsep", "topics": [ "guess_fitsep", "guess_fitsep.data.table", "guess_fitsep.SummarizedExperiment" ] }, { "page": "guess_maxquant_quantity", "title": "Guess maxquant quantity from snames", "topics": [ "guess_maxquant_quantity" ] }, { "page": "guess_sep", "title": "Guess separator", "topics": [ "guess_sep", "guess_sep.character", "guess_sep.factor", "guess_sep.numeric", "guess_sep.SummarizedExperiment" ] }, { "page": "has_multiple_levels", "title": "Variable has multiple levels?", "topics": [ "has_multiple_levels", "has_multiple_levels.character", "has_multiple_levels.data.table", "has_multiple_levels.factor", "has_multiple_levels.numeric", "has_multiple_levels.SummarizedExperiment" ] }, { "page": "hdlproteins", "title": "hdl proteomewatch proteins", "topics": [ "hdlproteins" ] }, { "page": "impute", "title": "Impute", "topics": [ "impute", "impute.matrix", "impute.numeric", "impute.SummarizedExperiment" ] }, { "page": "installed", "title": "Is package installed?", "topics": [ "installed" ] }, { "page": "invert_subgroups", "title": "Invert subgroups", "topics": [ "invert_subgroups" ] }, { "page": "is_character_matrix", "title": "Is character matrix", "topics": [ "assert_character_matrix", "is_character_matrix" ] }, { "page": "is_collapsed_subset", "title": "Is collapsed subset", "topics": [ "is_collapsed_subset" ] }, { "page": "is_compounddiscoverer_output", "title": "Is compounddiscoverer output?", "topics": [ "is_compounddiscoverer_output" ] }, { "page": "is_correlation_matrix", "title": "Assert correlation matrix", "topics": [ "assert_correlation_matrix", "is_correlation_matrix" ] }, { "page": "is_diann_report", "title": "Is diann report ?", "topics": [ "assert_compounddiscoverer_output", "assert_diann_report", "assert_fragpipe_tsv", "assert_maxquant_phosphosites", "assert_maxquant_proteingroups", "is_diann_report" ] }, { "page": "is_fastadt", "title": "Is fastadt", "topics": [ "assert_fastadt", "is_fastadt" ] }, { "page": "is_file", "title": "Is a file?", "topics": [ "is_file" ] }, { "page": "is_fraction", "title": "Is fraction", "topics": [ "assert_is_fraction", "is_fraction" ] }, { "page": "is_fragpipe_tsv", "title": "Is fragpipe file?", "topics": [ "is_fragpipe_tsv" ] }, { "page": "is_imputed", "title": "Get/set is_imputed", "topics": [ "is_imputed", "is_imputed,SummarizedExperiment-method", "is_imputed<-", "is_imputed<-,SummarizedExperiment,matrix-method", "is_imputed<-,SummarizedExperiment,NULL-method" ] }, { "page": "is_maxquant_phosphosites", "title": "Is maxquant phosphosites file?", "topics": [ "is_maxquant_phosphosites" ] }, { "page": "is_maxquant_proteingroups", "title": "Is maxquant proteingroups file?", "topics": [ "is_maxquant_proteingroups" ] }, { "page": "all_non_numeric", "title": "Are all variables non-numeric ?", "topics": [ "all_non_numeric", "is_non_numeric" ] }, { "page": "is_positive_number", "title": "Is positive number", "topics": [ "assert_positive_number", "assert_weakly_positive_number", "is_positive_number", "is_weakly_positive_number" ] }, { "page": "is_scalar_subset", "title": "Is scalar subset", "topics": [ "assert_scalar_subset", "is_scalar_subset" ] }, { "page": "is_sig", "title": "Is significant?", "topics": [ "is_sig" ] }, { "page": "is_valid_formula", "title": "Is valid formula", "topics": [ "assert_valid_formula", "is_valid_formula" ] }, { "page": "keep_estimable_features", "title": "Keep estimable features", "topics": [ "keep_estimable_features" ] }, { "page": "label2index", "title": "Convert labels into indices", "topics": [ "label2index" ] }, { "page": "factor.vars", "title": "Get factor variables", "topics": [ "factor.vars", "factor.vars,formula,data.table-method", "factor.vars,formula,SummarizedExperiment-method", "left.vars", "right.vars" ] }, { "page": "LINMOD", "title": "General Linear Model", "topics": [ "fit_limma", "fit_lm", "fit_lme", "fit_lmer", "fit_wilcoxon", "LINMOD", "linmod_limma", "linmod_lm", "linmod_lme", "linmod_lmer", "linmod_wilcoxon" ] }, { "page": "LINMODENGINES", "title": "Linear Modeling Engines", "topics": [ "LINMODENGINES" ] }, { "page": "list_files", "title": "list files", "topics": [ "list_files" ] }, { "page": "list2mat", "title": "list to matrix", "topics": [ "list2mat" ] }, { "page": "log2counts", "title": "Get/Set log2counts", "topics": [ "log2counts", "log2counts,SummarizedExperiment-method", "log2counts<-", "log2counts<-,SummarizedExperiment,matrix-method", "log2counts<-,SummarizedExperiment,numeric-method" ] }, { "page": "log2cpm", "title": "Get/Set log2cpm", "topics": [ "log2cpm", "log2cpm,SummarizedExperiment-method", "log2cpm<-", "log2cpm<-,SummarizedExperiment,matrix-method", "log2cpm<-,SummarizedExperiment,numeric-method" ] }, { "page": "log2diffs", "title": "Get/Set log2diffs", "topics": [ "log2diffs", "log2diffs,SummarizedExperiment-method", "log2diffs<-", "log2diffs<-,SummarizedExperiment,matrix-method", "log2diffs<-,SummarizedExperiment,numeric-method" ] }, { "page": "log2proteins", "title": "Get/Set log2proteins", "topics": [ "log2proteins", "log2proteins,SummarizedExperiment-method", "log2proteins<-", "log2proteins<-,SummarizedExperiment,matrix-method", "log2proteins<-,SummarizedExperiment,numeric-method" ] }, { "page": "log2sites", "title": "Get/Set log2sites", "topics": [ "log2sites", "log2sites,SummarizedExperiment-method", "log2sites<-", "log2sites<-,SummarizedExperiment,matrix-method", "log2sites<-,SummarizedExperiment,numeric-method" ] }, { "page": "log2tpm", "title": "Get/Set log2tpm", "topics": [ "log2tpm", "log2tpm,SummarizedExperiment-method", "log2tpm<-", "log2tpm<-,SummarizedExperiment,matrix-method", "log2tpm<-,SummarizedExperiment,numeric-method" ] }, { "page": "log2transform", "title": "Transform values", "topics": [ "exp2transform", "fscale", "invnorm", "log2transform", "quantnorm", "sscale", "vsn", "zscore" ] }, { "page": "logical2factor", "title": "logical to factor", "topics": [ "factor2logical", "logical2factor" ] }, { "page": "make_alpha_palette", "title": "Make alpha palette", "topics": [ "make_alpha_palette" ] }, { "page": "make_colors", "title": "Make colors", "topics": [ "make_colors" ] }, { "page": "make_volcano_dt", "title": "Create volcano datatable", "topics": [ "make_volcano_dt" ] }, { "page": "map_fvalues", "title": "Map fvalues", "topics": [ "map_fvalues" ] }, { "page": "matrix2sumexp", "title": "Convert matrix into SummarizedExperiment", "topics": [ "matrix2sumexp" ] }, { "page": "MAXQUANT_PATTERNS", "title": "maxquant quantity patterns", "topics": [ "MAXQUANT_PATTERNS" ] }, { "page": "mclust_breaks", "title": "Mixture/Quantile breaks", "topics": [ "mclust_breaks", "mixtools_breaks", "quantile_breaks" ] }, { "page": "fcor", "title": "Feature correlations/distances", "topics": [ "fcor", "fdist", "mdsplot", "scor", "sdist" ] }, { "page": "merge_compounddiscoverer", "title": "merge compound discoverer files", "topics": [ "merge_compounddiscoverer" ] }, { "page": "merge_sample_excel", "title": "Merge sample excel", "topics": [ "merge_sample_excel" ] }, { "page": "merge_sample_file", "title": "Merge sample / feature file", "topics": [ "merge_ffile", "merge_sample_file" ] }, { "page": "merge_sdata", "title": "Merge sample/feature dt", "topics": [ "merge_fdata", "merge_fdt", "merge_sdata", "merge_sdt" ] }, { "page": "message_df", "title": "message dataframe", "topics": [ "message_df" ] }, { "page": "modelvar", "title": "Get model variable", "topics": [ "abstractvar", "abstractvar.data.table", "abstractvar.SummarizedExperiment", "abstractvec", "abstractvec.data.table", "abstractvec.SummarizedExperiment", "downfeatures", "effectdt", "effectmat", "effectsizemat", "effectvar", "effectvec", "fdrmat", "fdrvar", "fdrvec", "modeldt", "modeldt.data.table", "modeldt.NULL", "modeldt.SummarizedExperiment", "modelfeatures", "modelfeatures.data.table", "modelfeatures.SummarizedExperiment", "modelmat", "modelvar", "modelvar.data.table", "modelvar.NULL", "modelvar.SummarizedExperiment", "modelvec", "modelvec.data.table", "modelvec.SummarizedExperiment", "pdt", "pmat", "pvar", "pvec", "tdt", "tmat", "tvar", "tvec", "upfeatures" ] }, { "page": "MSIGCOLLECTIONSHUMAN", "title": "Human/Mouse Msigdb Collections", "topics": [ "MSIGCOLLECTIONSHUMAN", "MSIGCOLLECTIONSMOUSE" ] }, { "page": "MSIGDIR", "title": "local msigdb dir", "topics": [ "MSIGDIR" ] }, { "page": "split_extract_fixed", "title": "stri_split and extract", "topics": [ "nfactors", "split_extract", "split_extract_fixed", "split_extract_regex" ] }, { "page": "object1", "title": "Example objects for binding", "topics": [ "object1", "object2" ] }, { "page": "OPENTARGETSDIR", "title": "opentargets dir", "topics": [ "OPENTARGETSDIR" ] }, { "page": "order_on_p", "title": "Order on p", "topics": [ "order_on_effect", "order_on_p", "order_on_t" ] }, { "page": "overall_parameters", "title": "Distribution parameters", "topics": [ "mclust_parameters", "mixtools_parameters", "overall_parameters" ] }, { "page": "pca", "title": "PCA, SMA, LDA, PLS, SPLS, OPLS", "topics": [ "lda", "opls", "pca", "pls", "sma", "spls" ] }, { "page": "pg_to_canonical", "title": "proteingroup to isoforms", "topics": [ "pg_to_canonical", "pg_to_isoforms" ] }, { "page": "plot_coef_densities", "title": "Plot contrast densities", "topics": [ "plot_coef_densities" ] }, { "page": "plot_contrast_venn", "title": "Plot contrast venn", "topics": [ "plot_contrast_venn" ] }, { "page": "plot_contrastogram", "title": "Plot contrastogram", "topics": [ "plot_contrastogram" ] }, { "page": "plot_data", "title": "Plot data", "topics": [ "plot_data" ] }, { "page": "plot_densities", "title": "Plot sample/feature distributions", "topics": [ "plot_densities", "plot_feature_densities", "plot_sample_densities" ] }, { "page": "explore-transforms", "title": "Visually evaluate transformation effects", "topics": [ "biplot_transforms", "biplot_transforms_assays", "plot_densities_transforms", "plot_violins_transforms" ] }, { "page": "plot_design", "title": "Plot model", "topics": [ "plot_design" ] }, { "page": "plot_exprs", "title": "Plot exprs for coef", "topics": [ "plot_exprs", "plot_feature_boxplots", "plot_sample_boxplots" ] }, { "page": "plot_exprs_per_coef", "title": "Plot exprs per coef", "topics": [ "plot_exprs_per_coef" ] }, { "page": "plot_fit_summary", "title": "Plot fit summary", "topics": [ "plot_fit_summary" ] }, { "page": "plot_heatmap", "title": "Plot heatmap", "topics": [ "plot_heatmap" ] }, { "page": "plot_matrix", "title": "Plot binary matrix", "topics": [ "plot_matrix" ] }, { "page": "plot_detections", "title": "Plot (summarized) detections", "topics": [ "plot_detections", "plot_sample_nas", "plot_subgroup_nas", "plot_summarized_detections" ] }, { "page": "plot_subgroup_points", "title": "Plot features", "topics": [ "plot_subgroup_points" ] }, { "page": "plot_summary", "title": "Plot summary", "topics": [ "plot_summary" ] }, { "page": "plot_venn", "title": "Plot venn", "topics": [ "plot_venn" ] }, { "page": "plot_venn_heatmap", "title": "Plot venn heatmap", "topics": [ "plot_venn_heatmap" ] }, { "page": "plot_violins", "title": "Plot sample/feature violins", "topics": [ "plot_feature_violins", "plot_sample_violins", "plot_subgroup_violins", "plot_violins" ] }, { "page": "plot_volcano", "title": "Plot volcano", "topics": [ "plot_volcano" ] }, { "page": "plot_xy_density", "title": "Plot xy densities", "topics": [ "plot_xy_density", "plot_xy_scatter", "plot_x_density", "plot_y_density" ] }, { "page": "PRECURSOR_QUANTITY", "title": "diann precursor quantity", "topics": [ "PRECURSOR_QUANTITY" ] }, { "page": "preprocess_rnaseq_counts", "title": "Preprocess RNAseq counts", "topics": [ "preprocess_rnaseq_counts" ] }, { "page": "pull_columns", "title": "Pull columns in a dataframe to the front", "topics": [ "pull_columns" ] }, { "page": "pvalues_estimable", "title": "Are coefs/pvalues estimable", "topics": [ "coefs_estimable", "pvalues_estimable" ] }, { "page": "read_affymetrix", "title": "Read affymetrix microarray", "topics": [ "read_affymetrix" ] }, { "page": "read_compounddiscoverer", "title": "Read compound discoverer output", "topics": [ "read_compounddiscoverer" ] }, { "page": "read_diann_phosphodiffs", "title": "Read diann phosphosites", "topics": [ "read_diann_pgmatrix", "read_diann_phosphodiffs", "read_diann_phosphosites" ] }, { "page": "read_fragpipe", "title": "Read fragpipe", "topics": [ "read_fragpipe" ] }, { "page": "read_maxquant_phosphosites", "title": "Read maxquant phosphosites", "topics": [ "read_maxquant_phosphosites", "read_phosphosites" ] }, { "page": "read_maxquant_proteingroups", "title": "Read maxquant proteingroups", "topics": [ "read_maxquant_proteingroups", "read_proteingroups" ] }, { "page": "read_msigdt", "title": "Read msigdb datatable", "topics": [ "read_msigdt" ] }, { "page": "read_olink", "title": "Read olink file", "topics": [ "read_olink" ] }, { "page": "read_salmon", "title": "Read salmon", "topics": [ "read_salmon" ] }, { "page": "read_uniprotdt", "title": "Read fasta hdrs", "topics": [ "parse_maxquant_hdrs", "read_contaminantdt", "read_uniprotdt" ] }, { "page": "reset_fit", "title": "Reset fit", "topics": [ "reset_fit" ] }, { "page": "rm_diann_contaminants", "title": "Rm contaminants", "topics": [ "rm_diann_contaminants" ] }, { "page": "rm_missing_in_some_samples", "title": "Rm features missing in some samples", "topics": [ "rm_missing_in_all_samples", "rm_missing_in_some_samples" ] }, { "page": "rm_unmatched_samples", "title": "rm unmatched/singleton samples", "topics": [ "rm_singleton_samples", "rm_unmatched_samples" ] }, { "page": "sbind", "title": "Sample/Feature/Assay bind", "topics": [ "abind", "fbind", "sbind" ] }, { "page": "scaledlibsizes", "title": "Get tmm-scaled libsizes", "topics": [ "scaledlibsizes" ] }, { "page": "scoremat", "title": "Extract scores/loadings", "topics": [ "loadingmat", "loadings", "scoremat", "scores" ] }, { "page": "slevels", "title": "Get slevels", "topics": [ "slevels", "subgroup_levels" ] }, { "page": "snames", "title": "Get/Set snames", "topics": [ "snames", "snames,SummarizedExperiment-method", "snames<-", "snames<-,SummarizedExperiment,character-method" ] }, { "page": "split_samples", "title": "Split samples", "topics": [ "cbind_imputed", "split_features", "split_samples" ] }, { "page": "stepauc", "title": "Compute step auc", "topics": [ "stepauc" ] }, { "page": "stri_any_regex", "title": "Does any string have a regex", "topics": [ "stri_any_regex" ] }, { "page": "stri_detect_fixed_in_collapsed", "title": "Detect fixed patterns in collapsed strings", "topics": [ "stri_detect_fixed_in_collapsed" ] }, { "page": "subgroup_matrix", "title": "Get subgroup matrix", "topics": [ "subgroup_array", "subgroup_matrix" ] }, { "page": "subtract_baseline", "title": "Subtract baseline", "topics": [ "subtract_baseline", "subtract_differences", "subtract_pairs" ] }, { "page": "sumexp_to_tsv", "title": "Write sumexp to tsv", "topics": [ "sumexp_to_tsv" ] }, { "page": "sumexp_to_longdt", "title": "SummarizedExperiment to data.table", "topics": [ "sumexp_to_groupdt", "sumexp_to_longdt", "sumexp_to_widedt" ] }, { "page": "sumexplist_to_longdt", "title": "SummarizedExperiment list to long data.table", "topics": [ "sumexplist_to_longdt" ] }, { "page": "summarize_fit", "title": "Summarize fit", "topics": [ "summarize_fit", "summarize_fit.data.table", "summarize_fit.SummarizedExperiment" ] }, { "page": "survobj", "title": "Survival analysis example", "topics": [ "survobj" ] }, { "page": "svalues", "title": "Get/Set svalues", "topics": [ "sampleid_values", "subgroup_values", "svalues", "svalues<-", "svalues<-,SummarizedExperiment,character-method" ] }, { "page": "svars", "title": "Get/Set svars", "topics": [ "svars", "svars,MultiAssayExperiment-method", "svars,SummarizedExperiment-method", "svars<-", "svars<-,MultiAssayExperiment,character-method", "svars<-,SummarizedExperiment,character-method" ] }, { "page": "systematic_nas", "title": "Is systematic/random/full NA", "topics": [ "no_nas", "random_nas", "systematic_nas" ] }, { "page": "tag_features", "title": "Tag features", "topics": [ "tag_features" ] }, { "page": "tag_hdlproteins", "title": "Tag hdlproteins", "topics": [ "tag_hdlproteins" ] }, { "page": "TAXON_TO_ORGNAME", "title": "Annotation Maps", "topics": [ "ABBREV_TO_ORGNAME", "EXISTENCE_TO_NUMBER", "REVIEWED_TO_NUMBER", "TAXON_TO_ORGNAME" ] }, { "page": "TESTS", "title": "Statistical models supported in autonomics", "topics": [ "TESTS" ] }, { "page": "tpm", "title": "Get/Set tpm", "topics": [ "tpm", "tpm,SummarizedExperiment-method", "tpm<-", "tpm<-,SummarizedExperiment,matrix-method", "tpm<-,SummarizedExperiment,numeric-method" ] }, { "page": "TRANSFORMENGINES", "title": "Data Transformation Methods", "topics": [ "TRANSFORMENGINES", "TRANSFORMSTRICT" ] }, { "page": "twofactor_sumexp", "title": "twofactor sumexp", "topics": [ "twofactor_sumexp" ] }, { "page": "uncollapse", "title": "Uncollapse/Recollapse", "topics": [ "recollapse", "uncollapse" ] }, { "page": "values", "title": "Get/Set expr values", "topics": [ "values", "values,SummarizedExperiment-method", "values<-", "values<-,SummarizedExperiment,matrix-method", "values<-,SummarizedExperiment,numeric-method" ] }, { "page": "varlevels_dont_clash", "title": "Are varlevels unique", "topics": [ "varlevels_dont_clash", "varlevels_dont_clash.data.table", "varlevels_dont_clash.SummarizedExperiment" ] }, { "page": "venn_detects", "title": "Venn detects", "topics": [ "venn_detects" ] }, { "page": "weights", "title": "Get/Set weights", "topics": [ "weights", "weights,SummarizedExperiment-method", "weights<-", "weights<-,SummarizedExperiment,matrix-method", "weights<-,SummarizedExperiment,NULL-method", "weights<-,SummarizedExperiment,numeric-method" ] }, { "page": "write_xl", "title": "Write xl", "topics": [ "write_ods", "write_xl" ] }, { "page": "X", "title": "Model based prediction", "topics": [ "beta", "X" ] }, { "page": "zero_to_na", "title": "Change nondetect representation", "topics": [ "inf_to_na", "minusinf_to_na", "nan_to_na", "na_to_string", "na_to_zero", "zero_to_na" ] } ], "_readme": "https://github.com/bioc/autonomics/raw/HEAD/README.md", "_rundeps": [ "abind", "affy", "affyio", "arrow", "askpass", "assertthat", "base64enc", "Biobase", "BiocBaseUtils", "BiocFileCache", "BiocGenerics", "BiocManager", "bit", "bit64", "blob", "boot", "cachem", "cellranger", "cli", "cluster", "codingMatrices", "colorspace", "cpp11", "crayon", "curl", "data.table", "DBI", "dbplyr", "DelayedArray", "dplyr", "edgeR", "farver", "fastmap", "filelock", "fractional", "generics", "GenomicRanges", "ggforce", "ggplot2", "ggrepel", "glue", "gridExtra", "gtable", "hms", "httr2", "IRanges", "isoband", "jsonlite", "labeling", "lattice", "lifecycle", "limma", "lme4", "locfit", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "minqa", "MultiAssayExperiment", "nlme", "nloptr", "openssl", "pillar", "pkgconfig", "polyclip", "preprocessCore", "prettyunits", "progress", "purrr", "R.methodsS3", "R.oo", "R.utils", "R6", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppEigen", "Rdpack", "readxl", "reformulas", "rematch", "rlang", "RSQLite", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "SparseArray", "statmod", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "systemfonts", "tibble", "tidyr", "tidyselect", "tweenr", "utf8", "vctrs", "viridisLite", "vsn", "withr", "XVector" ], "_vignettes": [ { "source": "autonomics_platformaware_analysis.Rmd", "filename": "autonomics_platformaware_analysis.html", "title": "autonomics: platform-aware analysis", "engine": "knitr::rmarkdown", "headings": [ "Abstract", "RNAseq", "read_rnaseq_counts", "read_rnaseq_bams", "cpm/tmm/voom effects on power", "Proteingroups/phosphosites", "LFQ intensities", "Normalized ratios", "Metabolon", "Somascan", "SessionInfo", "References" ], "created": "2023-12-15 13:08:43", "modified": "2024-11-04 12:53:01", "commits": 10 } ], "_score": 5.707570176097937, "_indexed": true, "_nocasepkg": "autonomics", "_universes": [ "bioc", "bhagwataditya" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.21.0", "date": "2026-05-29T08:54:45.000Z", "distro": "noble", "commit": "67b8f93b5e98c966f2ee80b844acf9c554d53590", "fileid": 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