.read_maxquant          Read/Analyze proteingroups/phosphosites
.read_metabolon         Read metabolon
.read_rectangles        Read omics data from rectangular file
.read_rnaseq_bams       Read rnaseq
.read_somascan          Read somascan
AUTONOMICS_DATASETS     Data used in examples/vignette/tests/longtests
MAXQUANT_PATTERNS_PEPCOUNTS
                        maxquant peptide count patterns
MAXQUANT_PATTERNS_QUANTITY
                        maxquant quantity patterns
TESTS                   Statistical models supported in autonomics
add_smiles              Add smiles
analysis                Get/set analysis
analyze                 Analyze
assert_is_valid_sumexp
                        Assert that x is a valid SummarizedExperiment
biplot                  Biplot
center                  Center samples
contrast_subgroup_cols
                        Row/Col contrasts
contrastdefs            Get/set contrastdefs
counts                  Get/Set counts
counts2cpm              Convert between counts and cpm
counts2tpm              counts to tpm
cpm                     Get/Set cpm
create_design           Create design
create_sfile            Create sfile
default_sfile           Default sfile
default_subgroupvar     Create default formula
download_data           Download autonomics example data
download_gtf            Download GTF file
dt2mat                  'data.table' to 'matrix'
explore_imputations     Explore imputations
explore_transformations
                        Explore transformations
extract_features        Extract features
extract_rectangle       Extract rectangle from omics file, data.table,
                        or matrix
fdata                   Get/Set fdata
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_replicated       Filter for replicated features
filter_samples          Filter samples on condition
fit_limma               Fit model and test for differential expression
flevels                 Get fvar levels
fnames                  Get/Set fnames
formula2str             formula to string
fvalues                 Get fvalues
fvars                   Get/Set fvars
guess_maxquant_quantity
                        Guess maxquant quantity from snames
guess_sep               Guess separator
impute_systematic_nondetects
                        Impute systematic nondetects
invert                  Invert
is_imputed              Get/set is_imputed
is_sig                  Is significant?
limma                   Get/set limma results
log2counts              Get/Set log2counts
log2countsratios        Get/Set log2countsratios
log2cpm                 Get/Set log2cpm
log2cpmratios           Get/Set log2cpmratios
log2tpm                 Get/Set log2tpm
log2tpmratios           Get/Set log2tpmratios
log2transform           Transform values
make_volcano_dt         Create volcano datatable
matrix2sumexp           Convert matrix into SummarizedExperiment
merge_sdata             Merge sample/feature data
merge_sfile             Merge sample/feature file
message_df              message dataframe
nfactors                stri_split and extract
normimpute              Impute from half-normal distribution around 0
occupancies             Get/Set occupancies
pca                     Add PCA, SMA, LDA, PLS
plot_boxplots           Plot sample/feature boxplots
plot_contrastogram      Plot contrastogram
plot_corrections        Biplot batch corrections
plot_covariates         Biplot covariates
plot_data               Plot data
plot_densities          Plot sample/feature densities
plot_detects            Plot detections
plot_features           Plot features
plot_venn               Plot venn
plot_violins            Plot sample/feature violins
plot_volcano            Plot volcano
preprocess_rnaseq_counts
                        Preprocess RNAseq counts
proteingroups           Get/Set proteingroups
read_affymetrix         Read affymetrix microarray
rm_singleton_samples    Rm singleton samples
scaledlibsizes          Get tmm-scaled libsizes
sdata                   Get/Set sdata
slevels                 Get slevels
snames                  Get/Set snames
split_by_svar           Split by svar
standardize_maxquant_snames
                        Standardize maxquant snames
subgroup_array          Get subgroup matrix
subtract_baseline       Subtract baseline
sumexp2mae              Create MultiAssayExperiment from
                        SummarizedExperiment list
sumexp_to_wide_dt       Convert SummarizedExperiment into data.table
summarize_fit           Summarize fit
svalues                 Get/Set svalues
svars                   Get/Set svars
tpm                     Get/Set tpm
values                  Get/Set expr values
venn_detects            Venn detects
weights                 Get/Set weights
zero_to_na              Change nondetect representation
