API for bhagwataditya/autonomics
Unified Statistical Modeling of Omics Data

Global functions
%<>%	Man page
%>%	Man page
.cbindstats	Source code
.extract_effectsize_features	Man page
.extract_fdr_features	Man page
.extract_n_features	Man page
.extract_p_features	Man page
.extract_sign_features	Man page
.filter_medoid	Source code
.filter_minvar	Source code
.fit_limma	Man page
.is_collapsed_subset	Source code
.is_numeric	Source code
.merge	Man page
.pg_to_canonical	Source code
.pg_to_isoforms	Source code
.plot_exprs	Source code
.plot_survival	Man page
.read_compounddiscoverer	Man page Source code
.read_compounddiscoverer_masslist	Man page Source code
.read_diann_precursors	Man page
.read_diann_proteingroups	Man page
.read_fragpipe_fdt	Source code
.read_fragpipe_mat	Source code
.read_maxquant_phosphosites	Man page Source code
.read_maxquant_proteingroups	Man page Source code
.read_metabolon	Man page Source code
.read_rectangles	Man page Source code
.read_rnaseq_bams	Man page
.read_rnaseq_counts	Man page
.read_somascan	Man page Source code
.read_spectronaut_sites	Source code
.subtract_baseline	Source code
.wilcoxon_onesample	Source code
ABBREV_TO_ORGNAME	Man page
AUTONOMICS_DATASETS	Man page
COMPOUNDDISCOVERER_PATTERNS	Man page
CONTAMINANTSURL	Man page
DATADIR	Man page
DIM	Source code
DIMRED	Man page
DIMREDSUPER	Man page
DIMREDUN	Man page
EXISTENCE_TO_NUMBER	Man page
FITSEP	Man page
LINMOD_ENGINES	Man page
MAXQUANT_PATTERNS	Man page
MSIGCOLLECTIONSHUMAN	Man page
MSIGCOLLECTIONSMOUSE	Man page
MSIGDIR	Man page
OPENTARGETSDIR	Man page
PPATTERN	Man page
PRECURSOR_QUANTITY	Man page
REVIEWED_TO_NUMBER	Man page
TAXON_TO_ORGNAME	Man page
TESTS	Man page
X	Man page Source code
`cause<-`	Source code
abstract_fit	Man page
abstractvar	Man page
abstractvar.SummarizedExperiment	Man page
abstractvar.data.table	Man page
abstractvec	Man page
abstractvec.SummarizedExperiment	Man page
abstractvec.data.table	Man page
add_adjusted_pvalues	Man page
add_adjusted_pvalues.SummarizedExperiment	Man page
add_adjusted_pvalues.data.table	Man page
add_affy_fdata	Source code
add_assay_means	Man page
add_color_scale	Source code
add_facetvars	Man page Source code
add_fill_scale	Source code
add_highlights	Source code
add_kegg_pathways	Source code
add_opentargets_by_uniprot	Man page
add_psp	Man page
add_smiles	Man page Source code
add_subgroup	Source code
all_have_setidentical_colnames	Source code
altenrich	Man page
analysis	Man page
analysis,SummarizedExperiment-method	Man page
analysis<-	Man page
analysis<-,SummarizedExperiment,list-method	Man page
analyze	Man page Source code
annotate_compounddiscoverer	Man page
annotate_maxquant	Man page
annotate_uniprot_rest	Man page
are_disjoint_sets	Source code
are_factor	Source code
are_identical	Source code
are_same_length	Source code
are_set_equal	Source code
assert_all_are_dirs	Source code
assert_all_are_existing_files	Source code
assert_all_are_greater_than	Source code
assert_all_are_in_left_open_range	Source code
assert_all_are_in_range	Source code
assert_all_are_less_than_or_equal_to	Source code
assert_all_are_non_missing_nor_empty_character	Source code
assert_all_are_not_na	Source code
assert_all_are_true	Source code
assert_all_have_setidentical_colnames	Source code
assert_any_are_matching_regex	Source code
assert_any_are_true	Source code
assert_are_disjoint_sets	Source code
assert_are_identical	Source code
assert_are_same_length	Source code
assert_compounddiscoverer_output	Man page Source code
assert_correlation_matrix	Man page Source code
assert_diann_report	Man page Source code
assert_engine	Source code
assert_fastadt	Man page Source code
assert_fragpipe_tsv	Man page Source code
assert_has_duplicates	Source code
assert_has_names	Source code
assert_has_no_duplicates	Source code
assert_is_a_bool	Source code
assert_is_a_number	Source code
assert_is_a_string	Source code
assert_is_all_of	Source code
assert_is_character	Source code
assert_is_data.frame	Source code
assert_is_data.table	Source code
assert_is_empty	Source code
assert_is_factor	Source code
assert_is_formula	Source code
assert_is_fraction	Man page Source code
assert_is_function	Source code
assert_is_identical_to_false	Source code
assert_is_identical_to_true	Source code
assert_is_list	Source code
assert_is_logical	Source code
assert_is_matrix	Source code
assert_is_not_null	Source code
assert_is_numeric	Source code
assert_is_scalar	Source code
assert_is_subset	Source code
assert_is_valid_sumexp	Man page Source code
assert_maxquant_phosphosites	Man page Source code
assert_maxquant_proteingroups	Man page Source code
assert_positive_number	Man page Source code
assert_scalar_subset	Man page Source code
assert_valid_formula	Man page Source code
assert_weakly_positive_number	Man page Source code
assertionError	Source code
assertionMessage	Source code
assertionWarning	Source code
bapply	Source code
beta	Man page Source code
bin	Man page Source code
bin.SummarizedExperiment	Man page
bin.character	Man page Source code
bin.factor	Man page Source code
bin.logical	Man page Source code
bin.numeric	Man page Source code
biplot	Man page
biplot_corrections	Man page
biplot_covariates	Man page
block2lme	Man page
block2lme.character	Man page
block2lme.formula	Man page
block2lme.list	Man page
block_vars	Man page
call_and_name	Source code
cause	Source code
cbind_imputed	Man page Source code
cduplicated	Source code
center	Man page
cequals	Source code
character2factor	Source code
check_n	Source code
code	Man page Source code
code.data.table	Man page Source code
code.factor	Man page Source code
code_control	Man page Source code
code_deviation	Man page Source code
code_deviation_first	Man page Source code
code_diff	Man page Source code
code_diff_forward	Man page Source code
code_helmert	Man page Source code
code_helmert_forward	Man page Source code
coefs	Man page
coefs.SummarizedExperiment	Man page
coefs.data.table	Man page
coefs.factor	Man page
coerce_to	Source code
collapse_in	Man page
collapse_in.character	Man page
collapse_in.factor	Man page
collapse_in.list	Man page
collapsed_entrezg_to_symbol	Man page
commonify_strings	Source code
compute_connections	Source code
contains_ratios	Source code
contr.diff	Man page Source code
contr.treatment.explicit	Man page Source code
contrast_coefs	Source code
contrast_subgroup_cols	Man page Source code
contrast_subgroup_rows	Man page Source code
contrmat2list	Source code
contrvec2mat	Source code
count_in	Man page
count_in.character	Man page
count_in.factor	Man page
count_in.list	Man page
count_out	Man page
count_out.character	Man page
count_out.factor	Man page
count_out.list	Man page
counts	Man page
counts,SummarizedExperiment-method	Man page
counts2cpm	Man page
counts2tpm	Man page
counts<-	Man page
counts<-,SummarizedExperiment,NULL-method	Man page
counts<-,SummarizedExperiment,matrix-method	Man page
counts<-,SummarizedExperiment,numeric-method	Man page
cpm	Man page
cpm,SummarizedExperiment-method	Man page
cpm2counts	Man page
cpm<-	Man page
cpm<-,SummarizedExperiment,matrix-method	Man page
cpm<-,SummarizedExperiment,numeric-method	Man page
create_design	Man page Source code
create_design.SummarizedExperiment	Man page Source code
create_design.data.table	Man page Source code
data.table	Man page
default_coefs	Man page Source code
default_coefs.SummarizedExperiment	Man page Source code
default_coefs.data.table	Man page Source code
default_formula	Man page Source code
default_geom	Man page Source code
default_sfile	Man page Source code
default_subgroupvar	Man page Source code
default_subtitle	Source code
default_x	Source code
demultiplex	Man page
dequantify	Man page Source code
dequantify_compounddiscoverer	Man page
downfeatures	Man page
download_contaminants	Man page
download_data	Man page Source code
download_gtf	Man page Source code
download_mcclain21	Man page
download_tcga_example	Man page Source code
drop_differing_uniprots	Source code
dt2mat	Man page
effectdt	Man page
effectmat	Man page
effectsizemat	Man page
effectvar	Man page
effectvec	Man page
enrichment	Man page
ens2org	Man page
entrezg_to_symbol	Man page
evenify_upwards	Source code
exp2	Man page
extract	Man page
extract_coef_features	Man page
extract_common_substr	Source code
extract_dt_col	Source code
extract_dt_row	Source code
extract_fdata	Source code
extract_rectangle	Man page Source code
extract_rectangle.character	Man page Source code
extract_rectangle.data.table	Man page Source code
extract_rectangle.matrix	Man page Source code
extract_reviewed	Source code
extract_sdata	Source code
factor2logical	Man page
false	Source code
false_names	Source code
fcluster	Man page
fcor	Man page
fdata	Man page
fdata,SummarizedExperiment-method	Man page
fdata<-	Man page
fdata<-,SummarizedExperiment,data.frame-method	Man page
fdist	Man page
fdr2p	Man page Source code
fdrmat	Man page
fdrvar	Man page
fdrvec	Man page
fdt	Man page
fdt,SummarizedExperiment-method	Man page
fdt<-	Man page
fdt<-,SummarizedExperiment,data.table-method	Man page
fid_values	Source code
fid_var	Source code
filter_exprs_replicated_in_some_subgroup	Man page
filter_feature_quality	Source code
filter_feature_type	Source code
filter_features	Man page Source code
filter_medoid	Man page Source code
filter_sample_quality	Source code
filter_sample_type	Source code
filter_samples	Man page
find_medoid	Source code
fit	Man page
fit_limma	Man page
fit_limma_contrastogram	Source code
fit_lm	Man page
fit_lme	Man page
fit_lmer	Man page
fit_lmx	Man page
fit_survival	Man page
fit_wilcoxon	Man page
fitcoefs	Man page
fitdt	Man page
fits	Man page
fits.SummarizedExperiment	Man page
fits.data.table	Man page
fitvars	Man page
fix_xlgenes	Man page
flevels	Man page Source code
flip_sign_if_all_exprs_are_negative	Source code
fnames	Man page
fnames,SummarizedExperiment-method	Man page
fnames<-	Man page
fnames<-,SummarizedExperiment,character-method	Man page
formula2lm	Man page
formula2lmer	Man page
formula2str	Man page
fscale	Man page
ftype	Man page
fvalues	Man page Source code
fvars	Man page
fvars,SummarizedExperiment-method	Man page
fvars<-	Man page
fvars<-,SummarizedExperiment,character-method	Man page
genome_to_orgdb	Man page
get_metric	Source code
get_name_in_parent	Source code
give_feedback	Source code
group_by_level	Man page
group_by_level.character	Man page
group_by_level.data.table	Man page
group_by_level.factor	Man page
guess_compounddiscoverer_quantity	Man page Source code
guess_fitsep	Man page
guess_fitsep.SummarizedExperiment	Man page
guess_fitsep.data.table	Man page
guess_maxquant_quantity	Man page Source code
guess_sep	Man page
guess_sep.SummarizedExperiment	Man page Source code
guess_sep.character	Man page Source code
guess_sep.factor	Man page Source code
guess_sep.numeric	Man page Source code
has_colnames	Source code
has_duplicates	Source code
has_elements	Source code
has_even_length	Source code
has_identical_values	Source code
has_multiple_levels	Man page Source code
has_multiple_levels.SummarizedExperiment	Man page Source code
has_multiple_levels.character	Man page Source code
has_multiple_levels.data.table	Man page Source code
has_multiple_levels.factor	Man page Source code
has_multiple_levels.numeric	Man page Source code
has_names	Source code
has_no_duplicates	Source code
has_odd_length	Source code
has_rownames	Source code
has_some_svalues	Source code
has_valid_fnames	Source code
has_valid_snames	Source code
hdlproteins	Man page Source code
impute	Man page Source code
impute.SummarizedExperiment	Man page Source code
impute.matrix	Man page Source code
impute.numeric	Man page Source code
inf_to_na	Man page Source code
invert_subgroups	Man page
invnorm	Man page
is2	Source code
is_a_bool	Source code
is_a_number	Source code
is_a_string	Source code
is_character	Source code
is_collapsed_subset	Man page Source code
is_compounddiscoverer_output	Man page Source code
is_correlation_matrix	Man page Source code
is_data.frame	Source code
is_data.table	Source code
is_diann_report	Man page Source code
is_dir	Source code
is_empty	Source code
is_even	Source code
is_excel_file	Source code
is_existing_file	Source code
is_factor	Source code
is_fastadt	Man page Source code
is_file	Man page Source code
is_fixed_col_file	Source code
is_formula	Source code
is_fraction	Man page Source code
is_fragpipe_tsv	Man page Source code
is_function	Source code
is_greater_than	Source code
is_greater_than_or_equal_to	Source code
is_identical_to_false	Source code
is_identical_to_true	Source code
is_imputed	Man page
is_imputed,SummarizedExperiment-method	Man page
is_imputed<-	Man page
is_imputed<-,SummarizedExperiment,NULL-method	Man page
is_imputed<-,SummarizedExperiment,matrix-method	Man page
is_imputed_feature	Source code
is_imputed_sample	Source code
is_in_closed_range	Source code
is_in_left_open_range	Source code
is_in_range	Source code
is_less_than_or_equal_to	Source code
is_list	Source code
is_logical	Source code
is_matching_regex	Source code
is_matrix	Source code
is_max	Source code
is_maxquant_phosphosites	Man page Source code
is_maxquant_proteingroups	Man page Source code
is_missing_or_empty_character	Source code
is_na	Source code
is_non_missing_nor_empty_character	Source code
is_non_scalar	Source code
is_not_na	Source code
is_not_null	Source code
is_numeric	Source code
is_numeric_string	Source code
is_odd	Source code
is_of_length	Source code
is_one_sided_formula	Source code
is_positive_number	Man page Source code
is_scalar	Source code
is_scalar_subset	Man page Source code
is_sig	Man page
is_square_matrix	Source code
is_subset	Source code
is_true	Source code
is_uniquely_empty	Source code
is_valid_formula	Man page Source code
is_valid_sumexp	Source code
is_weakly_positive_number	Man page Source code
keep_connected_blocks	Man page
keep_connected_features	Man page
keep_replicated_features	Man page
kegg_entry_to_pathways	Source code
label2index	Man page Source code
lda	Man page
list2mat	Man page Source code
list_files	Man page Source code
loadingmat	Man page Source code
loadingnames	Source code
loadings	Man page Source code
log2counts	Man page
log2counts,SummarizedExperiment-method	Man page
log2counts<-	Man page
log2counts<-,SummarizedExperiment,matrix-method	Man page
log2counts<-,SummarizedExperiment,numeric-method	Man page
log2cpm	Man page
log2cpm,SummarizedExperiment-method	Man page
log2cpm<-	Man page
log2cpm<-,SummarizedExperiment,matrix-method	Man page
log2cpm<-,SummarizedExperiment,numeric-method	Man page
log2diffs	Man page
log2diffs,SummarizedExperiment-method	Man page
log2diffs<-	Man page
log2diffs<-,SummarizedExperiment,matrix-method	Man page
log2diffs<-,SummarizedExperiment,numeric-method	Man page
log2proteins	Man page
log2proteins,SummarizedExperiment-method	Man page
log2proteins<-	Man page
log2proteins<-,SummarizedExperiment,matrix-method	Man page
log2proteins<-,SummarizedExperiment,numeric-method	Man page
log2sites	Man page
log2sites,SummarizedExperiment-method	Man page
log2sites<-	Man page
log2sites<-,SummarizedExperiment,matrix-method	Man page
log2sites<-,SummarizedExperiment,numeric-method	Man page
log2tpm	Man page
log2tpm,SummarizedExperiment-method	Man page
log2tpm<-	Man page
log2tpm<-,SummarizedExperiment,matrix-method	Man page
log2tpm<-,SummarizedExperiment,numeric-method	Man page
log2transform	Man page
logical2factor	Man page
make_alpha_palette	Man page
make_colors	Man page Source code
make_fvar_palette	Source code
make_gtf_url	Source code
make_onefactor_colors	Source code
make_range_string	Source code
make_svar_palette	Source code
make_twofactor_colors	Source code
make_var_palette	Source code
make_volcano_dt	Man page
map_fvalues	Man page Source code
mat2dt	Man page
matrix2sumexp	Man page
mdsplot	Man page
merge_compounddiscoverer	Man page
merge_data	Source code
merge_fdata	Man page Source code
merge_fdt	Man page Source code
merge_ffile	Man page Source code
merge_fit	Source code
merge_sample_excel	Man page Source code
merge_sample_file	Man page Source code
merge_sdata	Man page Source code
merge_sdt	Man page Source code
message_df	Man page Source code
methodname	Source code
minusinf_to_na	Man page Source code
model_coefs	Source code
modeldt	Man page
modeldt.SummarizedExperiment	Man page
modeldt.data.table	Man page
modelfeatures	Man page
modelfeatures.SummarizedExperiment	Man page
modelfeatures.data.table	Man page
modelmat	Man page
modelvar	Man page
modelvar.SummarizedExperiment	Man page
modelvar.data.table	Man page
modelvec	Man page
modelvec.SummarizedExperiment	Man page
modelvec.data.table	Man page
mqdt_to_mat	Source code
multilevel	Source code
n_elements	Source code
n_imputed_features	Source code
n_imputed_features_per_subgroup	Source code
n_imputed_samples	Source code
na_to_string	Man page Source code
na_to_zero	Man page Source code
nan_to_na	Man page Source code
ncols	Source code
nfactors	Man page Source code
nlevels	Source code
no_nas	Man page
nrows	Source code
numerify	Source code
opls	Man page
order_on_effect	Man page
order_on_p	Man page
parse_maxquant_hdrs	Man page
pca	Man page Source code
pdt	Man page
percentiles	Man page
pg_to_canonical	Man page Source code
pg_to_isoforms	Man page Source code
plot_contrast_trajectories	Source code
plot_contrast_types	Source code
plot_contrast_venn	Man page
plot_contrastogram	Man page Source code
plot_data	Man page Source code
plot_densities	Man page Source code
plot_design	Man page
plot_detections	Man page
plot_exprs	Man page Source code
plot_exprs_per_coef	Man page Source code
plot_feature_boxplots	Man page Source code
plot_feature_densities	Man page Source code
plot_feature_violins	Man page
plot_fit_summary	Man page
plot_heatmap	Man page
plot_joint_density	Man page
plot_matrix	Man page
plot_sample_boxplots	Man page Source code
plot_sample_densities	Man page Source code
plot_sample_nas	Man page
plot_sample_violins	Man page
plot_subgroup_nas	Man page
plot_subgroup_points	Man page Source code
plot_subgroup_violins	Man page
plot_summarized_detections	Man page
plot_summary	Man page Source code
plot_survival	Man page
plot_top_features	Source code
plot_top_samples	Source code
plot_top_volcano	Source code
plot_venn	Man page
plot_venn_heatmap	Man page
plot_violins	Man page Source code
plot_volcano	Man page
pls	Man page Source code
pmat	Man page
preprocess_rnaseq_counts	Man page
print_and_capture	Source code
pubchem_to_smiles	Source code
pull_columns	Man page Source code
pvar	Man page
pvec	Man page
quantnorm	Man page
random_nas	Man page
read_affymetrix	Man page Source code
read_compounddiscoverer	Man page
read_contaminantdt	Man page
read_contaminants	Man page
read_diann	Man page
read_diann_proteingroups	Man page
read_fragpipe	Man page
read_genex	Source code
read_maxquant_phosphosites	Man page Source code
read_maxquant_proteingroups	Man page Source code
read_metabolon	Man page Source code
read_msigdt	Man page Source code
read_olink	Man page Source code
read_phosphosites	Man page
read_proteingroups	Man page Source code
read_rectangles	Man page Source code
read_rnaseq_bams	Man page
read_rnaseq_counts	Man page
read_salmon	Man page
read_somascan	Man page Source code
read_spectronaut_sites	Source code
read_uniprotdt	Man page
recollapse	Man page
reexports	Man page
release_to_build	Source code
reset_fit	Man page Source code
rm_diann_contaminants	Man page
rm_missing_in_all_samples	Man page
rm_missing_in_some_samples	Man page
rm_na_columns	Source code
rm_single_value_columns	Source code
rm_singleton_samples	Man page Source code
rm_unmatched_samples	Man page Source code
safe_deparse	Source code
sampleid_values	Man page Source code
scaledlibsizes	Man page
scor	Man page
scoremat	Man page Source code
scorenames	Source code
scores	Man page Source code
sdata	Man page
sdata,SummarizedExperiment-method	Man page
sdata<-	Man page
sdata<-,SummarizedExperiment,DataFrame-method	Man page
sdata<-,SummarizedExperiment,data.frame-method	Man page
sdist	Man page
sdt	Man page
sdt,SummarizedExperiment-method	Man page
sdt<-	Man page
sdt<-,SummarizedExperiment,data.table-method	Man page
set_cause	Source code
single_subgroup	Source code
singlelevel	Source code
slevels	Man page Source code
sma	Man page Source code
snames	Man page
snames,SummarizedExperiment-method	Man page
snames<-	Man page
snames<-,SummarizedExperiment,character-method	Man page
split_extract	Man page Source code
split_extract_fixed	Man page Source code
split_extract_regex	Man page Source code
split_features	Man page
split_samples	Man page Source code
split_subgroup_levels	Source code
split_subgroup_values	Source code
split_values	Source code Source code
spls	Man page
sscale	Man page
stri_any_regex	Man page
stri_detect_fixed_in_collapsed	Man page
strip_attributes	Source code
subgroup_array	Man page Source code
subgroup_levels	Man page Source code
subgroup_matrix	Man page
subgroup_values	Man page Source code
subtract_baseline	Man page Source code
subtract_differences	Man page
subtract_pairs	Man page
sumexp_to_longdt	Man page
sumexp_to_subrep_dt	Man page
sumexp_to_tsv	Man page
sumexp_to_widedt	Man page Source code
sumexplist_to_longdt	Man page Source code
summarize_fit	Man page
summarize_fit.SummarizedExperiment	Man page
summarize_fit.data.table	Man page
svalues	Man page Source code
svalues<-	Man page
svalues<-,SummarizedExperiment,character-method	Man page
svars	Man page
svars,MultiAssayExperiment-method	Man page
svars,SummarizedExperiment-method	Man page
svars<-	Man page
svars<-,MultiAssayExperiment,character-method	Man page
svars<-,SummarizedExperiment,character-method	Man page
systematic_nas	Man page
tag_features	Man page
tag_hdlproteins	Man page Source code
taxon2org	Man page
tdt	Man page
tmat	Man page
to_names	Source code
top_coef	Source code
tpm	Man page
tpm,SummarizedExperiment-method	Man page
tpm<-	Man page
tpm<-,SummarizedExperiment,matrix-method	Man page
tpm<-,SummarizedExperiment,numeric-method	Man page
true_names	Source code
tvar	Man page
tvec	Man page
twofactor_sumexp	Man page
type_description	Source code
un_int64	Source code
uncollapse	Man page
upfeatures	Man page
use_first	Source code
values	Man page
values,SummarizedExperiment-method	Man page
values<-	Man page
values<-,SummarizedExperiment,matrix-method	Man page
values<-,SummarizedExperiment,numeric-method	Man page
variancenames	Source code
variances	Source code
varlevels_dont_clash	Man page
varlevels_dont_clash.SummarizedExperiment	Man page
varlevels_dont_clash.data.table	Man page
vectorize_contrasts	Source code
venn_detects	Man page
vsn	Man page
weights	Man page
weights,SummarizedExperiment-method	Man page
weights<-	Man page
weights<-,SummarizedExperiment,NULL-method	Man page
weights<-,SummarizedExperiment,matrix-method	Man page
weights<-,SummarizedExperiment,numeric-method	Man page
which.medoid	Source code
write_ods	Man page
write_xl	Man page
zero_to_na	Man page Source code
zscore	Man page