Files in bhagwataditya/importomics
Unified statistal Modeling of Omics Data
.BBSoptions
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
NEWS
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/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_plot_contrastogram.R
R/8_plot_volcano.R
R/9_annotate.R
README.md
_pkgdown.yml
inst/extdata/atkin.metabolon.xlsx
inst/extdata/atkin.somascan.adat
inst/extdata/fukuda20.proteingroups.txt
inst/scripts/00_prefetch.sh
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/CONTAMINANTSURL.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/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_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_formula.Rd
man/default_geom.Rd
man/default_sfile.Rd
man/demultiplex.Rd
man/dequantify.Rd
man/dot-merge.Rd
man/dot-plot_survival.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/explore_transformations.Rd
man/extract_coef_features.Rd
man/extract_rectangle.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/flevels.Rd
man/fnames.Rd
man/formula2str.Rd
man/fvalues.Rd
man/fvars.Rd
man/genome_to_orgdb.Rd
man/group_by_level.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_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/log2countsratios.Rd
man/log2cpm.Rd
man/log2cpmratios.Rd
man/log2diffs.Rd
man/log2proteins.Rd
man/log2sites.Rd
man/log2tpm.Rd
man/log2tpmratios.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_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_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_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/save_contaminant_hdrs.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/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-1.download.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/atkin19.svg
vignettes/autonomics_detailed_manual.Rmd
vignettes/autonomics_platformaware_analysis.Rmd
vignettes/autonomics_unified_modeling.Rmd
vignettes/references.bib
