API for bhagwataditya/importomics
Unified statistal 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_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
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
`cause<-` Source code
aa 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_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_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
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
explore_transformations 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
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
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
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_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_matrix Man page
plot_model_summary Man page Source code
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
prep_model_summary Source code
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
bhagwataditya/importomics documentation built on June 15, 2024, 1:05 a.m.