facilebio/FacileData
A fluent API for accessing multi-assay high-throughput genomics data

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Search the facilebio/FacileData package
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Functions
556
Source code
61
Man pages
105
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facilebio/FacileData: A fluent API for accessing multi-assay high-throughput genomics data
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API for facilebio/FacileData
A fluent API for accessing multi-assay high-throughput genomics data

Global functions
.create_wide_covariate_table Source code
.ds_annot_validate Source code
.extra_classes Source code
.extract_batch_terms Source code
.fetch_assay_data Source code
.gene_info Source code
.level_biotypes Man page Source code
.melt.assay.matrix Source code
.merge_ds_annot Source code
.parse_filter_vars Source code
.prepare_sample_covariates Man page Source code
.rlang_purrr_args_recycle Source code
.rlang_purrr_index Source code
.rlang_purrr_map_mold Source code
.rlang_purrr_probe Source code
.tidy.core Source code
.transcript_info Source code
FacileData Man page
FacileData-package Man page
FacileDataSet Man page Source code
accumulate Source code
accumulate_right Source code
adata Man page Source code
adata.DGEList Source code
adata.EList Source code
adata.ExpressionSet Source code
adata.SummarizedExperiment Source code
addFacileAssaySet Man page Source code
an_fds Man page Source code
anti_join Man page
anti_join.facile_frame Source code
append_facile_feature_info Man page Source code
append_facile_table Man page Source code
arrange Man page
arrange.facile_frame Source code
as.DGEList Man page Source code
as.DGEList.FacileDataSet Man page Source code
as.DGEList.data.frame Man page Source code
as.DGEList.facile_frame Man page Source code
as.DGEList.matrix Source code
as.DGEList.tbl Man page Source code
as.EAVtable Man page Source code
as.ExpressionSet Man page Source code
as.ExpressionSet.FacileDataSet Man page Source code
as.ExpressionSet.data.frame Man page Source code
as.FacileDataSet Man page Source code
as.FacileDataSet.default Source code
as.FacileDataSet.list Man page Source code
as.SummarizedExperiment Man page Source code
as.SummarizedExperiment.FacileDataSet Man page Source code
as.SummarizedExperiment.data.frame Man page Source code
as_Surv Man page Source code
as_cSurv Man page Source code
as_facile_frame Man page Source code
assay_feature_info_tbl Source code
assay_feature_info_tbl.FacileDataSet Source code
assay_feature_name_map Man page Source code
assay_feature_type Man page Source code
assay_info Man page Source code
assay_info.FacileDataSet Source code Source code
assay_info_tbl Source code
assay_info_tbl.FacileDataSet Source code
assay_names Source code
assay_names.FacileDataSet Source code
assay_names.default Source code
assay_names.facile_frame Source code
assay_sample_info Man page Source code
assay_sample_info.FacileDataSet Source code
assay_sample_info.facile_frame Source code
assay_sample_info_tbl Source code
assay_sample_info_tbl.FacileDataSet Source code
assay_sample_info_tbl.default Source code
assay_summary Man page Source code
assay_summary.FacileDataStore Source code
assay_summary.facile_frame Source code
assay_units Man page Source code
assay_units.FacileDataStore Source code
assembleFacileDataSet Man page Source code
assemble_example_dataset Man page Source code
assert_assay_feature_descriptor Man page Source code
assert_categorical Man page Source code
assert_columns Man page Source code
assert_covariate_definitions Man page Source code
assert_expression_result Man page Source code
assert_facet_descriptor Man page Source code
assert_facile_data_set Man page Source code
assert_facile_data_store Man page Source code
assert_facile_dataset_directory Source code
assert_sample_covariates Man page Source code
assert_sample_statistics Man page Source code
assert_sample_subset Man page Source code
assert_valid_assay_datasets Source code
assert_valid_meta_file Source code
bb.DGEList Source code
bb.EList Source code
bb.ExpressionSet Source code
bb.SummarizedExperiment Source code
bb.list Source code
bind_cols Man page
bind_rows Man page
biocbox Man page Source code
biocbox.FacileDataStore Source code
biocbox.facile_frame Man page Source code
biocbox_assay_class Source code
build_assay_list_file_path Man page Source code
build_assay_lists_load Man page Source code
build_available_assays Man page Source code
build_pb_split Man page Source code
cSurv Man page
can.spread.assay.by.name Source code
cast_covariate Man page Source code
check_categorical Man page Source code
check_facile_data_set Man page Source code
check_facile_data_store Man page Source code
check_facile_dataset_directory Source code
check_sample_subset Man page Source code
collect Man page
collect.facile_frame Source code
compact Source code
conform_data_frame Man page Source code
covariate_definitions Man page Source code
covariate_definitions.FacileDataSet Source code
covariate_meta_info Man page Source code
create_assay_feature_descriptor Man page Source code
dataset_definitions Man page Source code
dbfn Man page Source code
default_assay Source code
default_assay.FacileDataSet Man page Source code
default_assay.default Source code
detect Source code
detect_index Source code
discard Source code
distinct Man page
distinct.facile_frame Source code
downcast_ff Source code
ds_annot Man page Source code
ds_annot.ExpressionSet Source code
ds_annot.SummarizedExperiment Source code
ds_annot.default Source code
eav_decode_cSurv Man page Source code
eav_decode_categorical Man page Source code
eav_decode_logical Man page Source code
eav_decode_real Man page Source code
eav_decode_right_censored Man page Source code
eav_encode Man page Source code
eav_encode_cSurv Man page Source code
eav_encode_categorical Man page Source code
eav_encode_covariate Man page Source code
eav_encode_logical Man page Source code
eav_encode_real Man page Source code
eav_encode_right_censored Man page Source code
eav_metadata_create Man page Source code
eav_metadata_merge Man page Source code
eavdef_for_column Man page Source code
every Source code
exampleFacileDataSet Man page Source code
example_meta Man page Source code
example_sample_covariate_definitions Man page Source code
example_sample_covariates Man page Source code
executeSQL Man page Source code
extract.assay Source code
extract_transcribed_info_from_ensembl_gtf Man page Source code
facet_frame Man page Source code
facet_frame.FacileDataSet Man page Source code
facet_frame.default Source code
facilitate Man page Source code
fdata Man page Source code
fdata.DGEList Source code
fdata.EList Source code
fdata.ExpressionSet Source code
fdata.SummarizedExperiment Source code
fdebug Source code
fds Man page Source code
fds.FacileDataStore Man page Source code
fds.default Man page Source code
fds<- Man page
fds<-.data.frame Man page
fds<-.tbl Man page
feature_info_tbl Source code
feature_info_tbl.FacileDataSet Source code
feature_name_map Man page Source code
feature_types Man page Source code
features Man page Source code
features.FacileDataSet Source code
ferror Source code
fetch_assay_covariates Source code
fetch_assay_data Man page Source code
fetch_assay_data.FacileDataSet Source code
fetch_assay_data.default Source code
fetch_assay_data.facile_frame Source code
fetch_assay_score Man page Source code
fetch_assay_score.FacileDataSet Man page Source code
fetch_assay_score.default Source code
fetch_custom_sample_covariates Source code
fetch_custom_sample_covariates.FacileDataSet Man page Source code
fetch_custom_sample_covariates.default Source code
fetch_feature_info Source code
fetch_feature_info.FacileDataStore Source code
fetch_feature_info.default Source code
fetch_sample_covariates Man page Source code
fetch_sample_covariates.FacileDataSet Man page Source code
fetch_sample_covariates.default Source code
fetch_sample_covariates.facile_frame Man page Source code
fetch_sample_statistics Man page Source code
fetch_sample_statistics.FacileDataSet Man page Source code
fetch_sample_statistics.default Man page Source code
fetch_samples Source code
fetch_samples.FacileDataSet Man page Source code
fetch_samples.default Source code
ffatal Source code
filter Man page
filter.facile_frame Source code
filter_by_assay_support Man page Source code
filter_features Source code
filter_features.FacileDataSet Man page Source code
filter_features.default Source code
filter_samples Source code
filter_samples.FacileDataSet Man page Source code
filter_samples.default Source code
filter_samples.facile_frame Source code
finfo Source code
flog Man page Source code
flog_level Man page Source code
freplace_na Man page Source code
freplace_na.data.frame Source code
freplace_na.default Source code
freplace_na.list Source code
ftrace Source code
full_join.facile_frame Source code
fwarn Source code
gene_info_tbl Source code
gene_info_tbl.FacileDataSet Man page Source code
group_by Man page
group_by.facile_frame Source code Source code
group_map. Man page Source code
group_split. Man page Source code
group_split..data.frame Source code
group_split..grouped_df Source code
has_assay Man page Source code
has_assay.FacileDataStore Source code
has_assay.facile_frame Source code
has_columns Man page Source code
has_feature_type Man page Source code
hdf5fn Man page Source code
imap Source code
infer_feature_type Man page Source code
initializeFacileDataSet Man page Source code
inner_join Man page
inner_join.facile_frame Source code
is.FacileDataSet Man page Source code
is_assay_feature_descriptor Man page Source code
is_covariate_definitions Man page Source code
is_expression_result Man page Source code
is_facet_descriptor Man page Source code
is_sample_covariates Man page Source code
is_sample_statistics Man page Source code
join_samples Man page Source code
keep Source code
label Source code
label.NULL Source code
left_join Man page
left_join.facile_frame Source code
list_c Source code
map Source code
map2 Source code
map2_chr Source code
map2_dbl Source code
map2_int Source code
map2_lgl Source code
map_chr Source code
map_dbl Source code
map_if Source code
map_int Source code
map_lgl Source code
meta_file Man page Source code
meta_info Man page Source code
mutate Man page
mutate.facile_frame Source code
name Man page Source code
name.FacileDataSet Source code
name.NULL Source code
nameit Man page Source code
negate Source code
nest_join Man page
nest_join.facile_frame Source code
normalize_assay_data Man page Source code
normalize_assay_matrix.lognorm Source code
normalize_assay_matrix.qpcrct Source code
normalize_assay_matrix.qpcrdct Source code
normalize_assay_matrix.raw Source code
normalize_assay_matrix.rnaseq Source code
normalize_assay_matrix.tpm Source code
organism Source code
organism.FacileDataSet Man page Source code
organism.default Source code
organism.facile_frame Source code
parse_sample_criterion Man page Source code
pdata Man page Source code
pdata.DGEList Source code
pdata.EList Source code
pdata.ExpressionSet Source code
pdata.SummarizedExperiment Source code
pdata_metadata Man page Source code
pdata_metadata.DGEList Source code
pdata_metadata.EList Source code
pdata_metadata.ExpressionSet Source code
pdata_metadata.SummarizedExperiment Source code
pmap Source code
primary_key Man page Source code
print.FacileDataSet Source code
print.facile_frame Source code
reduce Source code
reduce_right Source code
reexports Man page
remove_batch_effect Man page Source code
rename Man page
rename.facile_frame Source code
reqpkg Source code
retrieve_samples_in_memory Source code
right_join.facile_frame Source code
sample_covariate_summary Man page Source code
sample_covariate_summary.FacileDataSet Source code
sample_covariate_summary.facile_frame Source code
sample_covariate_tbl Source code
sample_covariate_tbl.FacileDataSet Source code
sample_covariates.facile_frame Source code
sample_info_tbl Source code
sample_info_tbl.FacileDataSet Source code
sample_stats_tbl Source code
sample_stats_tbl.FacileDataSet Source code
samples Man page Source code
samples.FacileDataSet Man page Source code
samples.default Source code
samples.facile_frame Source code
samples_look_concordant Source code
save_custom_sample_covariates Man page Source code
select Man page
select.facile_frame Source code
semi_join Man page
semi_join.facile_frame Source code
set_class Man page Source code
set_fds Man page Source code
some Source code
some_celltypes Man page Source code
some_features Man page Source code
some_samples Man page Source code
spread_assay_data Man page Source code
spread_covariates Man page Source code
sqlFromFile Man page Source code
subset.facile_frame Source code
summarise Man page
summarize Man page
summary.eav_covariates Man page Source code
summary.wide_covariates Source code
supported.assay.container Source code
test_categorical Man page Source code
test_facile_data_set Man page Source code
test_facile_data_store Man page Source code
test_facile_dataset_directory Source code
test_sample_subset Man page Source code
tidy Man page
tidy.DGEList Source code
tidy.EList Source code
tidy.SummarizedExperiment Source code
tidy.matrix Source code
transmute Man page
transmute.facile_frame Source code
transpose Source code
ungroup Man page
ungroup.facile_frame Source code
upcast_ff Source code
validate.facile.dirs Source code
validate.fdata Source code
validate.pdata Source code
validate_covariate_def_list Man page Source code
walk Source code
with_assay_covariates Source code
with_assay_covariates.data.frame Source code
with_assay_covariates.facile_frame Source code
with_assay_data Source code
with_assay_data.data.frame Source code
with_assay_data.default Source code
with_assay_data.facile_frame Man page Source code
with_assay_data.tbl Source code
with_feature_info Man page Source code
with_feature_info.data.frame Source code
with_feature_info.default Source code
with_feature_info.facile_frame Source code
with_feature_info.tbl Source code
with_sample_covariates Man page Source code
with_sample_covariates.data.frame Source code
with_sample_covariates.default Source code
with_sample_covariates.facile_frame Source code
with_sample_covariates.tbl Source code
facilebio/FacileData documentation built on March 29, 2025, 4:30 p.m.

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