Files in facileverse/FacileData
A fluent API for accessing multi-assay high-throughput genomics data
.Rbuildignore
.github/.gitignore
.github/workflows/BiocCheck.yaml
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yaml
.github/workflows/test-coverage.yaml
.gitignore
DESCRIPTION
LICENSE.md
NAMESPACE
NEWS.md
R/FacileDataSet.R
R/NSE-filter-features.R
R/NSE-filter-samples.R
R/api.R
R/as.BiocAssayContainers.R
R/as.FacileDataSet.R
R/assay-data-FacileDataSet.R
R/assay-data.R
R/assay-support.R
R/assemble_example_dataset.R
R/biocbox.R
R/build-raw-data-assembly-helpers.R
R/construction.R
R/csurv.R
R/db-and-table-functions.R
R/entity-attribute-value.R
R/extract_transcribed_info_from_ensembl_gtf.R
R/facile_frame.R
R/feature-types.R
R/features-FacileDataSet.R
R/features.R
R/freplace_na.R
R/logging.R
R/normalize_assay_data.R
R/package.R
R/remove_batch_effect.R
R/sample-covariate-summary.R
R/sample-covariates.R
R/sample-info.R
R/samples.R
R/sql.R
R/test-helpers.R
R/tidy.R
R/utilities.R
R/validation.R
R/zzz.R
README.Rmd
README.md
TODO.Rmd
biocViews.txt
codecov.yml
inst/deprecated/create_FDS_pkg.R
inst/extdata/assay-data/scRNAseq-assay-list.qs
inst/extdata/assay-data/snRNAseq-assay-list.qs
inst/extdata/ensembl-v75-gene-info.csv.gz
inst/extdata/exampleFacileDataSet/custom-annotation/README.txt
inst/extdata/exampleFacileDataSet/data.h5
inst/extdata/exampleFacileDataSet/data.sqlite
inst/extdata/exampleFacileDataSet/meta.yaml
inst/extdata/feature-alias-map.human.csv
inst/extdata/feature-alias-map.mouse.csv
inst/extdata/init/faciledataset.sql
inst/extdata/test/sample-meta-definitions.yaml
inst/extdata/testFacileDataSet/custom-annotation/README.txt
inst/extdata/testFacileDataSet/data.h5
inst/extdata/testFacileDataSet/data.sqlite
inst/extdata/testFacileDataSet/meta.yaml
inst/presentations/facile-overview.key
inst/scrapbook/previous-FacileDataSet-creation.Rmd
inst/scripts/present-2023.Rmd
inst/scripts/retrieve-parathyroidSE-gene-info.R
inst/testdata/expected-meta.yaml
inst/testdata/generate-TCGA-tesdata.R
inst/testdata/test-sample-covariates.rds
man/FacileData-package.Rd
man/FacileDataSet.Rd
man/adata.Rd
man/addFacileAssaySet.Rd
man/an_fds.Rd
man/append_facile_feature_info.Rd
man/append_facile_table.Rd
man/as.BiocContainer.Rd
man/as.EAVtable.Rd
man/as.FacileDataSet.Rd
man/as_facile_frame.Rd
man/assay_feature_type.Rd
man/assay_info.Rd
man/assay_sample_info.Rd
man/assay_summary.Rd
man/assay_units.Rd
man/assembleFacileDataSet.Rd
man/assemble_example_dataset.Rd
man/assertions.Rd
man/biocbox.Rd
man/build_assay_list_file_path.Rd
man/build_assay_lists_load.Rd
man/build_available_assays.Rd
man/build_pb_split.Rd
man/cSurv.Rd
man/cast_covariate.Rd
man/check_categorical.Rd
man/check_facile_data_set.Rd
man/check_facile_data_store.Rd
man/conform_data_frame.Rd
man/covariate_definitions.Rd
man/covariate_meta_info.Rd
man/create_assay_feature_descriptor.Rd
man/dbfn.Rd
man/dot-level_biotypes.Rd
man/dot-prepare_sample_covariates.Rd
man/ds_annot.Rd
man/eav-metadata.Rd
man/eav-right-censor.Rd
man/eav_encode.Rd
man/eav_encode_covariate.Rd
man/eav_metadata_merge.Rd
man/eavdef_for_column.Rd
man/exampleFacileDataSet.Rd
man/executeSQL.Rd
man/extract_transcribed_info_from_ensembl_gtf.Rd
man/facet_frame.Rd
man/facilitate.Rd
man/fdata.Rd
man/fds.Rd
man/feature_name_map.Rd
man/feature_types.Rd
man/features.Rd
man/fetch_assay_data.Rd
man/fetch_assay_score.FacileDataSet.Rd
man/fetch_assay_score.Rd
man/fetch_custom_sample_covariates.FacileDataSet.Rd
man/fetch_sample_statistics.FacileDataSet.Rd
man/fetch_sample_statistics.Rd
man/fetch_sample_statistics.default.Rd
man/fetch_samples.FacileDataSet.Rd
man/figures/her2_cnv_vs_expression.png
man/filter_by_assay_support.Rd
man/filter_features.FacileDataSet.Rd
man/filter_samples.FacileDataSet.Rd
man/flog.Rd
man/flog_level.Rd
man/freplace_na.Rd
man/gene_info_tbl.FacileDataSet.Rd
man/has_assay.Rd
man/has_feature_type.Rd
man/hdf5fn.Rd
man/infer_feature_type.Rd
man/initializeFacileDataSet.Rd
man/is.FacileDataSet.Rd
man/join_samples.Rd
man/labeled.Rd
man/meta-info.Rd
man/nameit.Rd
man/normalize_assay_data.Rd
man/organism.FacileDataSet.Rd
man/parse_sample_criterion.Rd
man/pdata.Rd
man/pdata_metadata.Rd
man/primary_key.Rd
man/reexports.Rd
man/remove_batch_effect.Rd
man/sample-covariates.Rd
man/sample_covariate_summary.Rd
man/samples.FacileDataSet.Rd
man/samples.Rd
man/save_custom_sample_covariates.Rd
man/set_class.Rd
man/simple-eav-decode-functions.Rd
man/some_celltypes.Rd
man/some_features.Rd
man/some_samples.Rd
man/spread_assay_data.Rd
man/spread_covariates.Rd
man/sqlFromFile.Rd
man/summary.eav_covariates.Rd
man/test-helpers.Rd
man/validate_covariate_def_list.Rd
man/with_feature_info.Rd
pkgdown/extra.css
tests/README.md
tests/testthat.R
tests/testthat/test-EAV.R
tests/testthat/test-FacileDataSet.R
tests/testthat/test-as.FacileDataSet.R
tests/testthat/test-assay-data.R
tests/testthat/test-assay-info.R
tests/testthat/test-assay-normalization.R
tests/testthat/test-bioc-assay-containers.R
tests/testthat/test-biocbox.R
tests/testthat/test-csurv.R
tests/testthat/test-entity-attribute-value.R
tests/testthat/test-faciledataset-assembly.R
tests/testthat/test-feature-info.R
tests/testthat/test-feature-types.R
tests/testthat/test-remove-batch-effect.R
tests/testthat/test-replace_na.R
tests/testthat/test-sample-covariate-summaries.R
tests/testthat/test-sample-covariates.R
tests/testthat/test-samples.R
tests/testthat/testthat-problems.rds
vignettes/FacileData.Rmd
vignettes/FacileDataSet-architecture.Rmd
vignettes/FacileDataSet.Rmd
vignettes/archived/FacileDataSet-assembly.Rmd
vignettes/custom.css
vignettes/images/icons/INFO.txt
vignettes/images/icons/callout-border.png
vignettes/images/icons/callouts/1.png
vignettes/images/icons/callouts/10.png
vignettes/images/icons/callouts/11.png
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vignettes/images/icons/callouts/9.png
vignettes/images/icons/caution.png
vignettes/images/icons/download.png
vignettes/images/icons/example.png
vignettes/images/icons/home.png
vignettes/images/icons/important.png
vignettes/images/icons/next.png
vignettes/images/icons/note.png
vignettes/images/icons/prev.png
vignettes/images/icons/tip.png
vignettes/images/icons/up.png
vignettes/images/icons/warning.png
vignettes/images/icons/wip-full.png
vignettes/images/icons/wip.png
vignettes/raw-assay-data-assembly.Rmd
