.coxph                  Fit onefeature survival
.densities              Densities
.extract_p_features     Extract coefficient features
.fit_survival           Fit/Plot survival
.merge                  Clean Merge
.read_compounddiscoverer
                        Read compound discoverer files as-is
.read_compounddiscoverer_masslist
                        Read compound discoverer masslist files as-is
.read_diann_precursors
                        Read diann
.read_maxquant_proteingroups
                        Read proteingroups/phosphosites as-is
.read_metabolon         Read metabolon xlsxfile
.read_rectangles        Read omics data from rectangular file
.read_rnaseq_bams       Read rnaseq counts/bams
.read_somascan          Read somascan adatfile
abstract_fit            Abstract model fit
add_adjusted_pvalues    Add adjusted pvalues
add_assay_means         Add assay means
add_facetvars           Add facetvars
add_opentargets_by_uniprot
                        Add opentargets annotations
add_psp                 Add psp
add_smiles              Add smiles
altenrich               Alternative Enrichment Analysis
analysis                Get/set analysis
analyze                 Analyze
annotate_compounddiscoverer
                        Read compound discoverer output
annotate_maxquant       Annotate maxquant
annotate_uniprot_rest   Annotate uniprot/ensp
assert_is_valid_sumexp
                        Assert that x is a valid SummarizedExperiment
AUTONOMICS_DATASETS     Data used in examples/vignette/tests/longtests
awblinmod               General Linear Modeling (across-within-between
                        interface)
biplot                  Biplot
biplot_corrections      Biplot batch corrections
biplot_covariates       Biplot covariates
block_has_two_levels    Block has two levels
block2limma             block2limma
block2lm                block2lm
block2lme               block2lme
block2lmer              block2lmer
center                  Center samples
code                    Contrast Code Factor
collapsed_entrezg_to_symbol
                        Collapsed entrezg to genesymbol
COMPOUNDDISCOVERER_PATTERNS
                        compound discoverer quantity patterns
contrast_coefs          Get model coefs
contrast_subgroup_cols
                        Row/Col contrasts
contrastdt              Get contrastdt
count_in                Count/Collapse in/outside intersection
counts                  Get/Set counts
counts2cpm              Convert between counts and cpm/tpm
counts2tpm              counts to tpm
cpm                     Get/Set cpm
create_design           Create design matrix
DATADIR                 Download autonomics example data
default_formula         Create default formula
default_geom            Default geom
default_sfile           Default sfile
defaultmsigfile         Default msigdb file
demultiplex             Demultiplex snames
dequantify              Dequantify maxquant snames
dequantify_compounddiscoverer
                        dequantify_compounddiscoverer compound
                        discoverer snames
DIMREDUN                Dimension Reduction Methods
download_gtf            Download GTF file
download_mcclain21      Download mcclain21 data
dt2mat                  'data.table' to 'matrix'
enrichment              Enrichment analysis
ens2org                 taxon/ens to organism
entrezg_to_symbol       Entrezg to genesymbol
extract_rectangle       Extract rectangle from omics file, data.table,
                        or matrix
factorize               Factorize/Bin
fcluster                Cluster features
fdata                   Get/Set sample/feature data
fdr2p                   fdr to p
filter_exprs_replicated_in_some_subgroup
                        Filter features with replicated expression in
                        some subgroup
filter_features         Filter features on condition
filter_medoid           Filter medoid sample
filter_samples          Filter samples on condition
fits                    Get fit models
fix_xlgenes             Fix excel genes
flevels                 Get fvar levels
fnames                  Get/Set fnames
formula2str             formula to string
ftype                   Feature type
fvalues                 Get fvalues
fvars                   Get/Set fvars
genome_to_orgdb         Get corresponding orgdb
group_by_level          group by level
guess_compounddiscoverer_quantity
                        Guess compound discoverer quantity from snames
guess_fitsep            guess fitsep
guess_maxquant_quantity
                        Guess maxquant quantity from snames
guess_sep               Guess separator
has_multiple_levels     Variable has multiple levels?
hdlproteins             hdl proteomewatch proteins
impute                  Impute
installed               Is package installed?
invert_subgroups        Invert subgroups
is_character_matrix     Is character matrix
is_collapsed_subset     Is collapsed subset
is_compounddiscoverer_output
                        Is compounddiscoverer output?
is_correlation_matrix   Assert correlation matrix
is_diann_report         Is diann report ?
is_fastadt              Is fastadt
is_file                 Is a file?
is_fraction             Is fraction
is_fragpipe_tsv         Is fragpipe file?
is_imputed              Get/set is_imputed
is_maxquant_phosphosites
                        Is maxquant phosphosites file?
is_maxquant_proteingroups
                        Is maxquant proteingroups file?
is_non_numeric          Are all variables non-numeric ?
is_positive_number      Is positive number
is_scalar_subset        Is scalar subset
is_sig                  Is significant?
is_valid_formula        Is valid formula
keep_estimable_features
                        Keep estimable features
label2index             Convert labels into indices
left.vars               Get factor variables
LINMOD                  General Linear Model
LINMODENGINES           Linear Modeling Engines
list_files              list files
list2mat                list to matrix
log2counts              Get/Set log2counts
log2cpm                 Get/Set log2cpm
log2diffs               Get/Set log2diffs
log2proteins            Get/Set log2proteins
log2sites               Get/Set log2sites
log2tpm                 Get/Set log2tpm
log2transform           Transform values
logical2factor          logical to factor
make_alpha_palette      Make alpha palette
make_colors             Make colors
make_volcano_dt         Create volcano datatable
map_fvalues             Map fvalues
matrix2sumexp           Convert matrix into SummarizedExperiment
MAXQUANT_PATTERNS       maxquant quantity patterns
mclust_breaks           Mixture/Quantile breaks
mdsplot                 Feature correlations/distances
merge_compounddiscoverer
                        merge compound discoverer files
merge_sample_excel      Merge sample excel
merge_sample_file       Merge sample / feature file
merge_sdata             Merge sample/feature dt
message_df              message dataframe
modelvar                Get model variable
MSIGCOLLECTIONSHUMAN    Human/Mouse Msigdb Collections
MSIGDIR                 local msigdb dir
nfactors                stri_split and extract
object1                 Example objects for binding
OPENTARGETSDIR          opentargets dir
order_on_p              Order on p
overall_parameters      Distribution parameters
pca                     PCA, SMA, LDA, PLS, SPLS, OPLS
pg_to_canonical         proteingroup to isoforms
plot_coef_densities     Plot contrast densities
plot_contrast_venn      Plot contrast venn
plot_contrastogram      Plot contrastogram
plot_data               Plot data
plot_densities          Plot sample/feature distributions
plot_densities_transforms
                        Visually evaluate transformation effects
plot_design             Plot model
plot_exprs              Plot exprs for coef
plot_exprs_per_coef     Plot exprs per coef
plot_fit_summary        Plot fit summary
plot_heatmap            Plot heatmap
plot_matrix             Plot binary matrix
plot_sample_nas         Plot (summarized) detections
plot_subgroup_points    Plot features
plot_summary            Plot summary
plot_venn               Plot venn
plot_venn_heatmap       Plot venn heatmap
plot_violins            Plot sample/feature violins
plot_volcano            Plot volcano
plot_x_density          Plot xy densities
PRECURSOR_QUANTITY      diann precursor quantity
preprocess_rnaseq_counts
                        Preprocess RNAseq counts
pull_columns            Pull columns in a dataframe to the front
pvalues_estimable       Are coefs/pvalues estimable
read_affymetrix         Read affymetrix microarray
read_compounddiscoverer
                        Read compound discoverer output
read_diann_pgmatrix     Read diann phosphosites
read_fragpipe           Read fragpipe
read_maxquant_phosphosites
                        Read maxquant phosphosites
read_maxquant_proteingroups
                        Read maxquant proteingroups
read_msigdt             Read msigdb datatable
read_olink              Read olink file
read_salmon             Read salmon
read_uniprotdt          Read fasta hdrs
reset_fit               Reset fit
rm_diann_contaminants   Rm contaminants
rm_missing_in_all_samples
                        Rm features missing in some samples
rm_unmatched_samples    rm unmatched/singleton samples
sbind                   Sample/Feature/Assay bind
scaledlibsizes          Get tmm-scaled libsizes
scoremat                Extract scores/loadings
slevels                 Get slevels
snames                  Get/Set snames
split_samples           Split samples
stepauc                 Compute step auc
stri_any_regex          Does any string have a regex
stri_detect_fixed_in_collapsed
                        Detect fixed patterns in collapsed strings
subgroup_array          Get subgroup matrix
subtract_baseline       Subtract baseline
sumexp_to_tsv           Write sumexp to tsv
sumexp_to_widedt        SummarizedExperiment to data.table
sumexplist_to_longdt    SummarizedExperiment list to long data.table
summarize_fit           Summarize fit
survobj                 Survival analysis example
svalues                 Get/Set svalues
svars                   Get/Set svars
systematic_nas          Is systematic/random/full NA
tag_features            Tag features
tag_hdlproteins         Tag hdlproteins
TAXON_TO_ORGNAME        Annotation Maps
TESTS                   Statistical models supported in autonomics
tpm                     Get/Set tpm
TRANSFORMENGINES        Data Transformation Methods
twofactor_sumexp        twofactor sumexp
uncollapse              Uncollapse/Recollapse
values                  Get/Set expr values
varlevels_dont_clash    Are varlevels unique
venn_detects            Venn detects
weights                 Get/Set weights
write_xl                Write xl
X                       Model based prediction
zero_to_na              Change nondetect representation
