Abstract | RNAseq | read_rnaseq_counts | read_rnaseq_bams | cpm/tmm/voom effects on power | Proteingroups/phosphosites | LFQ intensities | Normalized ratios | Metabolon | Somascan | SessionInfo | References
Package: autonomics 1.21.0
Aditya Bhagwat
autonomics: Unified Statistical Modeling of Omics Data
This package unifies access to Statistal Modeling of Omics Data. Across linear modeling engines (lm, lme, lmer, limma, and wilcoxon). Across coding systems (treatment, difference, deviation, etc). Across model formulae (with/without intercept, random effect, interaction or nesting). Across omics platforms (microarray, rnaseq, msproteomics, affinity proteomics, metabolomics). Across projection methods (pca, pls, sma, lda, spls, opls). Across clustering methods (hclust, pam, cmeans). Across survival methods (coxph, survdiff, coin). It provides a fast enrichment analysis implementation.
Authors:
autonomics_1.21.0.tar.gz
autonomics_1.21.0.zip(r-4.7)autonomics_1.21.0.zip(r-4.6)autonomics_1.21.0.zip(r-4.5)
autonomics_1.21.0.tgz(r-4.6-any)autonomics_1.21.0.tgz(r-4.5-any)
autonomics_1.21.0.tar.gz(r-4.7-any)autonomics_1.21.0.tar.gz(r-4.6-any)
autonomics_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
autonomics/json (API)
| # Install 'autonomics' in R: |
| install.packages('autonomics', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:autonomics-1.21.0(bioc 3.24)autonomics-1.20.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
softwaredataimportpreprocessingdimensionreductionprincipalcomponentregressiondifferentialexpressiongenesetenrichmenttranscriptomicstranscriptiongeneexpressionrnaseqmicroarrayproteomicsmetabolomicsmassspectrometry
Last updated from:67b8f93b5e. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 325 | ||
| linux-devel-x86_64 | NOTE | 885 | ||
| source / vignettes | OK | 532 | ||
| linux-release-x86_64 | NOTE | 1125 | ||
| macos-release-arm64 | NOTE | 665 | ||
| macos-oldrel-arm64 | NOTE | 545 | ||
| windows-devel | NOTE | 1007 | ||
| windows-release | NOTE | 1032 | ||
| windows-oldrel | NOTE | 850 | ||
| wasm-release | OK | 290 |
Exports:.coxph.densities.extract_effectsize_features.extract_fdr_features.extract_n_features.extract_p_features.fit_survival.logrank.merge.read_compounddiscoverer.read_diann_precursors.read_diann_proteingroups.read_maxquant_phosphosites.read_maxquant_proteingroups.read_metabolon.read_rectangles.read_rnaseq_bams.read_rnaseq_counts.read_somascan.survdiff%<>%%>%ABBREV_TO_ORGNAMEabindabstract_fitabstractvarabstractvecadd_adjusted_pvaluesadd_assay_meansadd_facetvarsadd_opentargets_by_uniprotadd_pspadd_smilesall_non_numericaltenrichanalysisanalysis<-analyzeannotate_compounddiscovererannotate_maxquantannotate_uniprot_restassert_character_matrixassert_compounddiscoverer_outputassert_correlation_matrixassert_diann_reportassert_fastadtassert_fragpipe_tsvassert_is_fractionassert_is_valid_sumexpassert_maxquant_phosphositesassert_maxquant_proteingroupsassert_positive_numberassert_scalar_subsetassert_valid_formulaassert_weakly_positive_numberAUTONOMICS_DATASETSawblinmodawblinmod_limmaawblinmod_lmawblinmod_lmeawblinmod_lmerbetabinbin_assaybiplotbiplot_correctionsbiplot_covariatesbiplot_transformsbiplot_transforms_assaysblock_has_two_levelsblock2limmablock2lmblock2lmeblock2lmercbind_imputedcentercenter_meancenter_mediancodecode_controlcode_deviationcode_deviation_firstcode_diffcode_diff_forwardcode_helmertcode_helmert_forwardcoefscoefs_estimablecollapse_incollapsed_entrezg_to_symbolCOMPOUNDDISCOVERER_PATTERNScontr.diffcontr.treatment.explicitcontrast_coefscontrast_subgroup_colscontrast_subgroup_rowscontrastdtcount_incount_outcountscounts<-counts2cpmcounts2tpmcpmcpm<-cpm2countscreate_designdata.tableDATADIRdefault_formuladefault_geomdefault_sfiledefaultmsigfiledemultiplexdensitiesdequantifydequantify_compounddiscovererDIMREDENGINESDIMREDSUPERDIMREDUNdownfeaturesdownload_datadownload_gtfdownload_mcclain21dt2mateffectdteffectmateffectsizemateffectvareffectvecenrichmentens2orgentrezg_to_symbolEXISTENCE_TO_NUMBERexp2transformextractextract_contrast_featuresextract_rectanglefactor.varsfactor2logicalfactorizefactorize_assayfbindfclusterfcorfdatafdata<-fdistfdr2pfdrmatfdrvarfdrvecfdtfdt<-filter_exprs_replicated_in_some_subgroupfilter_featuresfilter_medoidfilter_samplesfit_limmafit_lmfit_lmefit_lmerfit_survivalfit_wilcoxonfitcoefsfitsfix_xlgenesflevelsfnamesfnames<-formula2strfscaleftypefvaluesfvarsfvars<-genome_to_orgdbgroup_by_levelguess_compounddiscoverer_quantityguess_fitsepguess_maxquant_quantityguess_sephas_multiple_levelshdlproteinsimputeinf_to_nainstalledinvert_subgroupsinvnormis_character_matrixis_collapsed_subsetis_compounddiscoverer_outputis_correlation_matrixis_diann_reportis_fastadtis_fileis_fractionis_fragpipe_tsvis_imputedis_imputed<-is_maxquant_phosphositesis_maxquant_proteingroupsis_non_numericis_positive_numberis_scalar_subsetis_sigis_valid_formulais_weakly_positive_numberkeep_estimable_featureslabel2indexldaleft.varsLINMODlinmod_limmalinmod_lmlinmod_lmelinmod_lmerlinmod_wilcoxonLINMODENGINESlist_fileslist2matloadingmatloadingslog2countslog2counts<-log2cpmlog2cpm<-log2diffslog2diffs<-log2proteinslog2proteins<-log2siteslog2sites<-log2tpmlog2tpm<-log2transformlogical2factormake_alpha_palettemake_colorsmake_volcano_dtmap_fvaluesmat2dtmatrix2sumexpMAXQUANT_PATTERNSmclust_breaksmclust_parametersmdsplotmerge_compounddiscoverermerge_fdatamerge_fdtmerge_ffilemerge_sample_excelmerge_sample_filemerge_sdatamerge_sdtmessage_dfminusinf_to_namixtools_breaksmixtools_parametersmodel_coefsmodeldtmodelfeaturesmodelmatmodelvarmodelvecMSIGCOLLECTIONSHUMANMSIGCOLLECTIONSMOUSEMSIGDIRna_to_stringna_to_zeronan_to_nanfactorsno_nasobject1object2OPENTARGETSDIRoplsorder_on_effectorder_on_porder_on_toverall_parametersparse_maxquant_hdrspcapdtpg_to_canonicalpg_to_isoformsplot_coef_densitiesplot_contrast_vennplot_contrastogramplot_dataplot_densitiesplot_densities_transformsplot_designplot_detectionsplot_exprsplot_exprs_per_coefplot_feature_boxplotsplot_feature_densitiesplot_feature_violinsplot_fit_summaryplot_heatmapplot_matrixplot_sample_boxplotsplot_sample_densitiesplot_sample_nasplot_sample_violinsplot_subgroup_nasplot_subgroup_pointsplot_subgroup_violinsplot_summarized_detectionsplot_summaryplot_survivalplot_vennplot_venn_heatmapplot_violinsplot_violins_transformsplot_volcanoplot_x_densityplot_xy_densityplot_xy_scatterplot_y_densityplspmatPRECURSOR_QUANTITYprep_survivalpreprocess_rnaseq_countspull_columnspvalues_estimablepvarpvecquantile_breaksquantnormrandom_nasread_affymetrixread_compounddiscovererread_contaminantdtread_diannread_diann_pgmatrixread_diann_phosphodiffsread_diann_phosphositesread_diann_proteingroupsread_fragpiperead_maxquant_phosphositesread_maxquant_proteingroupsread_metabolonread_msigdtread_olinkread_phosphositesread_proteingroupsread_rectanglesread_rnaseq_bamsread_rnaseq_countsread_salmonread_somascanread_uniprotdtrecollapsereset_fitREVIEWED_TO_NUMBERright.varsrm_diann_contaminantsrm_missing_in_all_samplesrm_missing_in_some_samplesrm_singleton_samplesrm_unmatched_samplessampleid_valuessbindscaledlibsizesscorscorematscoressdatasdata<-sdistsdtsdt<-slevelssmasnamessnames<-split_extractsplit_extract_fixedsplit_extract_regexsplit_featuressplit_samplessplssscalestepaucstri_any_regexstri_detect_fixed_in_collapsedsubgroup_arraysubgroup_levelssubgroup_matrixsubgroup_valuessubtract_baselinesubtract_differencessubtract_pairssumexp_to_groupdtsumexp_to_longdtsumexp_to_tsvsumexp_to_widedtsumexplist_to_longdtsummarize_fitsurvobjsvaluessvalues<-svarssvars<-systematic_nastag_featurestag_hdlproteinsTAXON_TO_ORGNAMEtaxon2orgtdtTESTStmattpmtpm<-TRANSFORMENGINESTRANSFORMSTRICTtvartvectwofactor_sumexpuncollapseupfeaturesvaluesvalues<-varlevels_dont_clashvenn_detectsvsnweightsweights<-write_odswrite_xlXzero_to_nazscore
Dependencies:abindaffyaffyioarrowaskpassassertthatbase64encBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerbitbit64blobbootcachemcellrangercliclustercodingMatricescolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydplyredgeRfarverfastmapfilelockfractionalgenericsGenomicRangesggforceggplot2ggrepelgluegridExtragtablehmshttr2IRangesisobandjsonlitelabelinglatticelifecyclelimmalme4locfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoiseminqaMultiAssayExperimentnlmenloptropensslpillarpkgconfigpolyclippreprocessCoreprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6rappdirsrbibutilsRColorBrewerRcppRcppEigenRdpackreadxlreformulasrematchrlangRSQLiteS4ArraysS4VectorsS7scalesSeqinfoSparseArraystatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstibbletidyrtidyselecttweenrutf8vctrsviridisLitevsnwithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Fit onefeature survival | .coxph .logrank .survdiff |
| Densities | .densities densities |
| Extract coefficient features | .extract_effectsize_features .extract_fdr_features .extract_n_features .extract_p_features extract_contrast_features |
| Fit/Plot survival | .fit_survival fit_survival plot_survival prep_survival |
| Clean Merge | .merge |
| Read compound discoverer files as-is | .read_compounddiscoverer |
| Read compound discoverer masslist files as-is | .read_compounddiscoverer_masslist |
| Read diann | .read_diann_precursors .read_diann_proteingroups read_diann read_diann_proteingroups |
| Read proteingroups/phosphosites as-is | .read_maxquant_phosphosites .read_maxquant_proteingroups |
| Read metabolon xlsxfile | .read_metabolon read_metabolon |
| Read omics data from rectangular file | .read_rectangles read_rectangles |
| Read rnaseq counts/bams | .read_rnaseq_bams .read_rnaseq_counts read_rnaseq_bams read_rnaseq_counts |
| Read somascan adatfile | .read_somascan read_somascan |
| Abstract model fit | abstract_fit |
| Add adjusted pvalues | add_adjusted_pvalues add_adjusted_pvalues.data.table add_adjusted_pvalues.NULL add_adjusted_pvalues.SummarizedExperiment |
| Add assay means | add_assay_means |
| Add facetvars | add_facetvars |
| Add opentargets annotations | add_opentargets_by_uniprot |
| Add psp | add_psp |
| Add smiles | add_smiles |
| Alternative Enrichment Analysis | altenrich |
| Get/set analysis | analysis analysis,SummarizedExperiment-method analysis<- analysis<-,SummarizedExperiment,list-method |
| Analyze | analyze |
| Read compound discoverer output | annotate_compounddiscoverer |
| Annotate maxquant | annotate_maxquant |
| Annotate uniprot/ensp | annotate_uniprot_rest |
| Assert that x is a valid SummarizedExperiment | assert_is_valid_sumexp |
| Data used in examples/vignette/tests/longtests | AUTONOMICS_DATASETS |
| General Linear Modeling (across-within-between interface) | awblinmod awblinmod_limma awblinmod_lm awblinmod_lme awblinmod_lmer |
| Biplot | biplot |
| Biplot batch corrections | biplot_corrections |
| Biplot covariates | biplot_covariates |
| Block has two levels | block_has_two_levels |
| block2limma | block2limma block2limma.character block2limma.formula block2limma.list block2limma.NULL |
| block2lm | block2lm block2lm.character block2lm.formula block2lm.list block2lm.NULL |
| block2lme | block2lme block2lme.character block2lme.formula block2lme.list |
| block2lmer | block2lmer block2lmer.character block2lmer.formula block2lmer.list |
| Center samples | center center_mean center_median |
| Contrast Code Factor | 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 |
| Collapsed entrezg to genesymbol | collapsed_entrezg_to_symbol |
| compound discoverer quantity patterns | COMPOUNDDISCOVERER_PATTERNS |
| Get model coefs | contrast_coefs model_coefs |
| Row/Col contrasts | contrast_subgroup_cols contrast_subgroup_rows |
| Get contrastdt | contrastdt |
| Count/Collapse in/outside intersection | 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 |
| Get/Set counts | counts counts,SummarizedExperiment-method counts<- counts<-,SummarizedExperiment,matrix-method counts<-,SummarizedExperiment,NULL-method counts<-,SummarizedExperiment,numeric-method |
| Convert between counts and cpm/tpm | counts2cpm cpm2counts |
| counts to tpm | counts2tpm |
| Get/Set cpm | cpm cpm,SummarizedExperiment-method cpm<- cpm<-,SummarizedExperiment,matrix-method cpm<-,SummarizedExperiment,numeric-method |
| Create design matrix | create_design create_design.data.table create_design.SummarizedExperiment |
| Download autonomics example data | DATADIR download_data |
| Create default formula | default_formula |
| Default geom | default_geom |
| Default sfile | default_sfile |
| Default msigdb file | defaultmsigfile |
| Demultiplex snames | demultiplex |
| Dequantify maxquant snames | dequantify |
| dequantify_compounddiscoverer compound discoverer snames | dequantify_compounddiscoverer |
| Dimension Reduction Methods | DIMREDENGINES DIMREDSUPER DIMREDUN |
| Download GTF file | download_gtf |
| Download mcclain21 data | download_mcclain21 |
| `data.table` to `matrix` | dt2mat mat2dt |
| Enrichment analysis | enrichment |
| taxon/ens to organism | ens2org taxon2org |
| Entrezg to genesymbol | entrezg_to_symbol |
| Extract rectangle from omics file, data.table, or matrix | extract_rectangle extract_rectangle.character extract_rectangle.data.table extract_rectangle.matrix |
| Factorize/Bin | 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 |
| Cluster features | fcluster |
| Get/Set sample/feature data | 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 |
| fdr to p | fdr2p |
| Filter features with replicated expression in some subgroup | filter_exprs_replicated_in_some_subgroup |
| Filter features on condition | filter_features |
| Filter medoid sample | filter_medoid |
| Filter samples on condition | filter_samples |
| Get fit models | coefs coefs.data.table coefs.factor coefs.NULL coefs.SummarizedExperiment fitcoefs fits fits.data.table fits.NULL fits.SummarizedExperiment |
| Fix excel genes | fix_xlgenes |
| Get fvar levels | flevels |
| Get/Set fnames | fnames fnames,SummarizedExperiment-method fnames<- fnames<-,SummarizedExperiment,character-method |
| formula to string | formula2str |
| Feature type | ftype |
| Get fvalues | fvalues |
| Get/Set fvars | fvars fvars,SummarizedExperiment-method fvars<- fvars<-,SummarizedExperiment,character-method |
| Get corresponding orgdb | genome_to_orgdb |
| group by level | group_by_level group_by_level.character group_by_level.data.table group_by_level.factor |
| Guess compound discoverer quantity from snames | guess_compounddiscoverer_quantity |
| guess fitsep | guess_fitsep guess_fitsep.data.table guess_fitsep.SummarizedExperiment |
| Guess maxquant quantity from snames | guess_maxquant_quantity |
| Guess separator | guess_sep guess_sep.character guess_sep.factor guess_sep.numeric guess_sep.SummarizedExperiment |
| Variable has multiple levels? | has_multiple_levels has_multiple_levels.character has_multiple_levels.data.table has_multiple_levels.factor has_multiple_levels.numeric has_multiple_levels.SummarizedExperiment |
| hdl proteomewatch proteins | hdlproteins |
| Impute | impute impute.matrix impute.numeric impute.SummarizedExperiment |
| Is package installed? | installed |
| Invert subgroups | invert_subgroups |
| Is character matrix | assert_character_matrix is_character_matrix |
| Is collapsed subset | is_collapsed_subset |
| Is compounddiscoverer output? | is_compounddiscoverer_output |
| Assert correlation matrix | assert_correlation_matrix is_correlation_matrix |
| Is diann report ? | assert_compounddiscoverer_output assert_diann_report assert_fragpipe_tsv assert_maxquant_phosphosites assert_maxquant_proteingroups is_diann_report |
| Is fastadt | assert_fastadt is_fastadt |
| Is a file? | is_file |
| Is fraction | assert_is_fraction is_fraction |
| Is fragpipe file? | is_fragpipe_tsv |
| Get/set is_imputed | is_imputed is_imputed,SummarizedExperiment-method is_imputed<- is_imputed<-,SummarizedExperiment,matrix-method is_imputed<-,SummarizedExperiment,NULL-method |
| Is maxquant phosphosites file? | is_maxquant_phosphosites |
| Is maxquant proteingroups file? | is_maxquant_proteingroups |
| Are all variables non-numeric ? | all_non_numeric is_non_numeric |
| Is positive number | assert_positive_number assert_weakly_positive_number is_positive_number is_weakly_positive_number |
| Is scalar subset | assert_scalar_subset is_scalar_subset |
| Is significant? | is_sig |
| Is valid formula | assert_valid_formula is_valid_formula |
| Keep estimable features | keep_estimable_features |
| Convert labels into indices | label2index |
| Get factor variables | factor.vars factor.vars,formula,data.table-method factor.vars,formula,SummarizedExperiment-method left.vars right.vars |
| General Linear Model | fit_limma fit_lm fit_lme fit_lmer fit_wilcoxon LINMOD linmod_limma linmod_lm linmod_lme linmod_lmer linmod_wilcoxon |
| Linear Modeling Engines | LINMODENGINES |
| list files | list_files |
| list to matrix | list2mat |
| Get/Set log2counts | log2counts log2counts,SummarizedExperiment-method log2counts<- log2counts<-,SummarizedExperiment,matrix-method log2counts<-,SummarizedExperiment,numeric-method |
| Get/Set log2cpm | log2cpm log2cpm,SummarizedExperiment-method log2cpm<- log2cpm<-,SummarizedExperiment,matrix-method log2cpm<-,SummarizedExperiment,numeric-method |
| Get/Set log2diffs | log2diffs log2diffs,SummarizedExperiment-method log2diffs<- log2diffs<-,SummarizedExperiment,matrix-method log2diffs<-,SummarizedExperiment,numeric-method |
| Get/Set log2proteins | log2proteins log2proteins,SummarizedExperiment-method log2proteins<- log2proteins<-,SummarizedExperiment,matrix-method log2proteins<-,SummarizedExperiment,numeric-method |
| Get/Set log2sites | log2sites log2sites,SummarizedExperiment-method log2sites<- log2sites<-,SummarizedExperiment,matrix-method log2sites<-,SummarizedExperiment,numeric-method |
| Get/Set log2tpm | log2tpm log2tpm,SummarizedExperiment-method log2tpm<- log2tpm<-,SummarizedExperiment,matrix-method log2tpm<-,SummarizedExperiment,numeric-method |
| Transform values | exp2transform fscale invnorm log2transform quantnorm sscale vsn zscore |
| logical to factor | factor2logical logical2factor |
| Make alpha palette | make_alpha_palette |
| Make colors | make_colors |
| Create volcano datatable | make_volcano_dt |
| Map fvalues | map_fvalues |
| Convert matrix into SummarizedExperiment | matrix2sumexp |
| maxquant quantity patterns | MAXQUANT_PATTERNS |
| Mixture/Quantile breaks | mclust_breaks mixtools_breaks quantile_breaks |
| Feature correlations/distances | fcor fdist mdsplot scor sdist |
| merge compound discoverer files | merge_compounddiscoverer |
| Merge sample excel | merge_sample_excel |
| Merge sample / feature file | merge_ffile merge_sample_file |
| Merge sample/feature dt | merge_fdata merge_fdt merge_sdata merge_sdt |
| message dataframe | message_df |
| Get model variable | 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 |
| Human/Mouse Msigdb Collections | MSIGCOLLECTIONSHUMAN MSIGCOLLECTIONSMOUSE |
| local msigdb dir | MSIGDIR |
| stri_split and extract | nfactors split_extract split_extract_fixed split_extract_regex |
| Example objects for binding | object1 object2 |
| opentargets dir | OPENTARGETSDIR |
| Order on p | order_on_effect order_on_p order_on_t |
| Distribution parameters | mclust_parameters mixtools_parameters overall_parameters |
| PCA, SMA, LDA, PLS, SPLS, OPLS | lda opls pca pls sma spls |
| proteingroup to isoforms | pg_to_canonical pg_to_isoforms |
| Plot contrast densities | plot_coef_densities |
| Plot contrast venn | plot_contrast_venn |
| Plot contrastogram | plot_contrastogram |
| Plot data | plot_data |
| Plot sample/feature distributions | plot_densities plot_feature_densities plot_sample_densities |
| Visually evaluate transformation effects | biplot_transforms biplot_transforms_assays plot_densities_transforms plot_violins_transforms |
| Plot model | plot_design |
| Plot exprs for coef | plot_exprs plot_feature_boxplots plot_sample_boxplots |
| Plot exprs per coef | plot_exprs_per_coef |
| Plot fit summary | plot_fit_summary |
| Plot heatmap | plot_heatmap |
| Plot binary matrix | plot_matrix |
| Plot (summarized) detections | plot_detections plot_sample_nas plot_subgroup_nas plot_summarized_detections |
| Plot features | plot_subgroup_points |
| Plot summary | plot_summary |
| Plot venn | plot_venn |
| Plot venn heatmap | plot_venn_heatmap |
| Plot sample/feature violins | plot_feature_violins plot_sample_violins plot_subgroup_violins plot_violins |
| Plot volcano | plot_volcano |
| Plot xy densities | plot_xy_density plot_xy_scatter plot_x_density plot_y_density |
| diann precursor quantity | PRECURSOR_QUANTITY |
| Preprocess RNAseq counts | preprocess_rnaseq_counts |
| Pull columns in a dataframe to the front | pull_columns |
| Are coefs/pvalues estimable | coefs_estimable pvalues_estimable |
| Read affymetrix microarray | read_affymetrix |
| Read compound discoverer output | read_compounddiscoverer |
| Read diann phosphosites | read_diann_pgmatrix read_diann_phosphodiffs read_diann_phosphosites |
| Read fragpipe | read_fragpipe |
| Read maxquant phosphosites | read_maxquant_phosphosites read_phosphosites |
| Read maxquant proteingroups | read_maxquant_proteingroups read_proteingroups |
| Read msigdb datatable | read_msigdt |
| Read olink file | read_olink |
| Read salmon | read_salmon |
| Read fasta hdrs | parse_maxquant_hdrs read_contaminantdt read_uniprotdt |
| Reset fit | reset_fit |
| Rm contaminants | rm_diann_contaminants |
| Rm features missing in some samples | rm_missing_in_all_samples rm_missing_in_some_samples |
| rm unmatched/singleton samples | rm_singleton_samples rm_unmatched_samples |
| Sample/Feature/Assay bind | abind fbind sbind |
| Get tmm-scaled libsizes | scaledlibsizes |
| Extract scores/loadings | loadingmat loadings scoremat scores |
| Get slevels | slevels subgroup_levels |
| Get/Set snames | snames snames,SummarizedExperiment-method snames<- snames<-,SummarizedExperiment,character-method |
| Split samples | cbind_imputed split_features split_samples |
| Compute step auc | stepauc |
| Does any string have a regex | stri_any_regex |
| Detect fixed patterns in collapsed strings | stri_detect_fixed_in_collapsed |
| Get subgroup matrix | subgroup_array subgroup_matrix |
| Subtract baseline | subtract_baseline subtract_differences subtract_pairs |
| Write sumexp to tsv | sumexp_to_tsv |
| SummarizedExperiment to data.table | sumexp_to_groupdt sumexp_to_longdt sumexp_to_widedt |
| SummarizedExperiment list to long data.table | sumexplist_to_longdt |
| Summarize fit | summarize_fit summarize_fit.data.table summarize_fit.SummarizedExperiment |
| Survival analysis example | survobj |
| Get/Set svalues | sampleid_values subgroup_values svalues svalues<- svalues<-,SummarizedExperiment,character-method |
| Get/Set svars | svars svars,MultiAssayExperiment-method svars,SummarizedExperiment-method svars<- svars<-,MultiAssayExperiment,character-method svars<-,SummarizedExperiment,character-method |
| Is systematic/random/full NA | no_nas random_nas systematic_nas |
| Tag features | tag_features |
| Tag hdlproteins | tag_hdlproteins |
| Annotation Maps | ABBREV_TO_ORGNAME EXISTENCE_TO_NUMBER REVIEWED_TO_NUMBER TAXON_TO_ORGNAME |
| Statistical models supported in autonomics | TESTS |
| Get/Set tpm | tpm tpm,SummarizedExperiment-method tpm<- tpm<-,SummarizedExperiment,matrix-method tpm<-,SummarizedExperiment,numeric-method |
| Data Transformation Methods | TRANSFORMENGINES TRANSFORMSTRICT |
| twofactor sumexp | twofactor_sumexp |
| Uncollapse/Recollapse | recollapse uncollapse |
| Get/Set expr values | values values,SummarizedExperiment-method values<- values<-,SummarizedExperiment,matrix-method values<-,SummarizedExperiment,numeric-method |
| Are varlevels unique | varlevels_dont_clash varlevels_dont_clash.data.table varlevels_dont_clash.SummarizedExperiment |
| Venn detects | venn_detects |
| Get/Set weights | weights weights,SummarizedExperiment-method weights<- weights<-,SummarizedExperiment,matrix-method weights<-,SummarizedExperiment,NULL-method weights<-,SummarizedExperiment,numeric-method |
| Write xl | write_ods write_xl |
| Model based prediction | beta X |
| Change nondetect representation | inf_to_na minusinf_to_na nan_to_na na_to_string na_to_zero zero_to_na |
