Files in bhagwataditya/autonomics

Unified Statistical Modeling of Omics Data

R/0_import.R R/10_survival.R R/11_enrichment.R R/1_assertions.R R/1_assertive.R R/1_download.R R/1_utilities.R R/2_filter.R R/2_get_set.R R/2_sumexp_to_dt.R R/3.0_read_omics.R R/3.1_read_rnaseq.R R/3.2_read_annotations.R R/3.2_read_proteingroups.R R/3.3_read_diann.R R/3.4_read_fragpipe.R R/3.5_read_spectronaut.R R/3.6_read_somascan.R R/3.7_read_metabolon.R R/3.8_read_compounddiscoverer.R R/4_analyze.R R/4_plot.R R/5_pca.R R/6_transform.R R/7_impute.R R/8_fit.R R/8_fit_limma.R R/8_fit_lmx.R R/8_fit_wilcoxon.R R/8_ftype.R R/8_plot_contrastogram.R R/8_plot_volcano.R R/9_annotate.R README.md inst/scripts/01_rnaseq.R inst/scripts/02_explore.R inst/scripts/03_contrast.R inst/scripts/04_phospho.R inst/scripts/9_cluster.R inst/scripts/advancedmodels.R inst/scripts/atkin_example.R inst/scripts/autonomics_for_somascan.Rmd inst/scripts/downsize.R inst/scripts/explore_pls_pca.R inst/scripts/graphicalabstract.R inst/scripts/history.R inst/scripts/multiple_fastafiles.R inst/scripts/poster.R inst/scripts/read_diann.R inst/scripts/sdata_augmentation.R longtests/LT3.1_rnaseq_bams.R longtests/LT3.2_proteingroups_1fasta.R longtests/LT8_fit.R man/AUTONOMICS_DATASETS.Rd man/COMPOUNDDISCOVERER_PATTERNS.Rd man/CONTAMINANTSURL.Rd man/DIMRED.Rd man/FITSEP.Rd man/LINMOD_ENGINES.Rd man/MAXQUANT_PATTERNS.Rd man/MSIGCOLLECTIONSHUMAN.Rd man/MSIGDIR.Rd man/OPENTARGETSDIR.Rd man/PRECURSOR_QUANTITY.Rd man/TAXON_TO_ORGNAME.Rd man/TESTS.Rd man/X.Rd man/abstract_fit.Rd man/add_adjusted_pvalues.Rd man/add_assay_means.Rd man/add_facetvars.Rd man/add_opentargets_by_uniprot.Rd man/add_psp.Rd man/add_smiles.Rd man/altenrich.Rd man/analysis.Rd man/analyze.Rd man/annotate_compounddiscoverer.Rd man/annotate_maxquant.Rd man/annotate_uniprot_rest.Rd man/assert_is_valid_sumexp.Rd man/bin.Rd man/biplot.Rd man/biplot_corrections.Rd man/biplot_covariates.Rd man/block2lme.Rd man/center.Rd man/code.Rd man/coefs.Rd man/collapsed_entrezg_to_symbol.Rd man/contrast_subgroup_cols.Rd man/count_in.Rd man/counts.Rd man/counts2cpm.Rd man/counts2tpm.Rd man/cpm.Rd man/create_design.Rd man/default_coefs.Rd man/default_formula.Rd man/default_geom.Rd man/default_sfile.Rd man/demultiplex.Rd man/dequantify.Rd man/dequantify_compounddiscoverer.Rd man/dot-merge.Rd man/dot-plot_survival.Rd man/dot-read_compounddiscoverer.Rd man/dot-read_compounddiscoverer_masslist.Rd man/dot-read_maxquant_proteingroups.Rd man/download_contaminants.Rd man/download_data.Rd man/download_gtf.Rd man/download_mcclain21.Rd man/download_tcga_example.Rd man/dt2mat.Rd man/enrichment.Rd man/entrezg_to_symbol.Rd man/extract_coef_features.Rd man/extract_rectangle.Rd man/fcluster.Rd man/fcor.Rd man/fdata.Rd man/fdr2p.Rd man/filter_exprs_replicated_in_some_subgroup.Rd man/filter_features.Rd man/filter_medoid.Rd man/filter_samples.Rd man/fit.Rd man/fit_lmx.Rd man/fitcoefs.Rd man/fits.Rd man/fitvars.Rd man/fix_xlgenes.Rd man/flevels.Rd man/fnames.Rd man/formula2str.Rd man/ftype.Rd man/fvalues.Rd man/fvars.Rd man/genome_to_orgdb.Rd man/group_by_level.Rd man/guess_compounddiscoverer_quantity.Rd man/guess_fitsep.Rd man/guess_maxquant_quantity.Rd man/guess_sep.Rd man/has_multiple_levels.Rd man/hdlproteins.Rd man/impute.Rd man/invert_subgroups.Rd man/is_collapsed_subset.Rd man/is_correlation_matrix.Rd man/is_diann_report.Rd man/is_fastadt.Rd man/is_file.Rd man/is_fraction.Rd man/is_imputed.Rd man/is_positive_number.Rd man/is_scalar_subset.Rd man/is_sig.Rd man/is_valid_formula.Rd man/keep_connected_blocks.Rd man/keep_connected_features.Rd man/keep_replicated_features.Rd man/label2index.Rd man/list2mat.Rd man/list_files.Rd man/log2counts.Rd man/log2cpm.Rd man/log2diffs.Rd man/log2proteins.Rd man/log2sites.Rd man/log2tpm.Rd man/log2transform.Rd man/logical2factor.Rd man/make_alpha_palette.Rd man/make_colors.Rd man/make_volcano_dt.Rd man/map_fvalues.Rd man/matrix2sumexp.Rd man/merge_compounddiscoverer.Rd man/merge_sample_excel.Rd man/merge_sample_file.Rd man/merge_sdata.Rd man/message_df.Rd man/modelvar.Rd man/order_on_p.Rd man/pca.Rd man/percentiles.Rd man/pg_to_canonical.Rd man/plot_contrast_venn.Rd man/plot_contrastogram.Rd man/plot_data.Rd man/plot_densities.Rd man/plot_design.Rd man/plot_exprs.Rd man/plot_exprs_per_coef.Rd man/plot_fit_summary.Rd man/plot_heatmap.Rd man/plot_joint_density.Rd man/plot_matrix.Rd man/plot_sample_nas.Rd man/plot_subgroup_points.Rd man/plot_summary.Rd man/plot_venn.Rd man/plot_venn_heatmap.Rd man/plot_violins.Rd man/plot_volcano.Rd man/preprocess_rnaseq_counts.Rd man/pull_columns.Rd man/read_affymetrix.Rd man/read_compounddiscoverer.Rd man/read_contaminants.Rd man/read_diann_proteingroups.Rd man/read_fragpipe.Rd man/read_maxquant_phosphosites.Rd man/read_maxquant_proteingroups.Rd man/read_metabolon.Rd man/read_msigdt.Rd man/read_olink.Rd man/read_rectangles.Rd man/read_rnaseq_counts.Rd man/read_salmon.Rd man/read_somascan.Rd man/read_uniprotdt.Rd man/reexports.Rd man/reset_fit.Rd man/rm_diann_contaminants.Rd man/rm_missing_in_some_samples.Rd man/rm_unmatched_samples.Rd man/scaledlibsizes.Rd man/scoremat.Rd man/slevels.Rd man/snames.Rd man/split_extract_fixed.Rd man/split_samples.Rd man/stri_any_regex.Rd man/stri_detect_fixed_in_collapsed.Rd man/subgroup_matrix.Rd man/subtract_baseline.Rd man/sumexp_to_longdt.Rd man/sumexp_to_tsv.Rd man/sumexplist_to_longdt.Rd man/summarize_fit.Rd man/svalues.Rd man/svars.Rd man/systematic_nas.Rd man/tag_features.Rd man/tag_hdlproteins.Rd man/taxon2org.Rd man/tpm.Rd man/twofactor_sumexp.Rd man/uncollapse.Rd man/values.Rd man/varlevels_dont_clash.Rd man/venn_detects.Rd man/weights.Rd man/write_xl.Rd man/zero_to_na.Rd tests/testthat.R tests/testthat/test-3.1_rnaseq_counts.R tests/testthat/test-3.2_proteingroups.R tests/testthat/test-3.4_somascan.R tests/testthat/test-3.5_metabolon.R tests/testthat/test-4_plot.R tests/testthat/test-8_fit.R vignettes/autonomics_platformaware_analysis.Rmd wignettes/autonomics_detailed_manual.Rmd wignettes/autonomics_unified_modeling.Rmd