ENCODExplorer: A compilation of ENCODE metadata

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This package allows user to quickly access ENCODE project files metadata and give access to helper functions to query the ENCODE rest api, download ENCODE datasets and save the database in SQLite format.

Author
Charles Joly Beauparlant [aut, cre], Audrey Lemacon [aut], Arnaud Droit [aut], Louis Gendron [ctb], Astrid-Louise Deschenes [ctb]
Date of publication
None
Maintainer
Charles Joly Beauparlant <charles.joly-beauparlant@crchul.ulaval.ca>
License
Artistic-2.0
Version
2.0.2

View on Bioconductor

Man pages

accession_df
Metadata from the ENCODE database in a R object. The tables...
clean_column
Clean a single column of the data.frame
clean_table
Clean a data.frame that was produced by extract_table
createDesign
Create a design for the files associated with the result of a...
downloadEncode
downloadEncode is use to download a serie of files or dataset...
encode_df
Metadata from the ENCODE database in a R object. The tables...
ENCODExplorer
ENCODExplorer
export_ENCODEdb_matrix
Extract essential informations from a list of data.table in a...
extract_table
Extract a data.frame corresponding to a table in ENCODE...
fuzzySearch
Fuzzysearch is a searching function for a string or a list of...
get_encode_types
A list of known tables from ENCODE database.
get_schemas
Extract the schemas from ENCODE's github
prepare_ENCODEdb
Create the list of data.table for the tables in ENCODE
queryEncode
Produce a subset of data following predefined criteria
searchEncode
Simulate a query on ENCODE website and return the result as a...
searchToquery
Convert searchEncode output in queryEncode output.

Files in this package

ENCODExplorer/DESCRIPTION
ENCODExplorer/NAMESPACE
ENCODExplorer/NEWS
ENCODExplorer/R
ENCODExplorer/R/ENCODExplorer.R
ENCODExplorer/R/createDesign.R
ENCODExplorer/R/download.R
ENCODExplorer/R/fuzzySearch.R
ENCODExplorer/R/prepare_data.R
ENCODExplorer/R/query.R
ENCODExplorer/R/rest_api.R
ENCODExplorer/R/shiny_encode.R
ENCODExplorer/README.md
ENCODExplorer/build
ENCODExplorer/build/vignette.rds
ENCODExplorer/data
ENCODExplorer/data/accession_df.rda
ENCODExplorer/data/datalist
ENCODExplorer/data/encode_df.rda
ENCODExplorer/inst
ENCODExplorer/inst/doc
ENCODExplorer/inst/doc/DBmodel.R
ENCODExplorer/inst/doc/DBmodel.Rmd
ENCODExplorer/inst/doc/DBmodel.html
ENCODExplorer/inst/doc/DataUpdate.R
ENCODExplorer/inst/doc/DataUpdate.Rmd
ENCODExplorer/inst/doc/DataUpdate.html
ENCODExplorer/inst/doc/ENCODExplorer.R
ENCODExplorer/inst/doc/ENCODExplorer.Rmd
ENCODExplorer/inst/doc/ENCODExplorer.html
ENCODExplorer/inst/extdata
ENCODExplorer/inst/extdata/ABC_df_lab.rda
ENCODExplorer/inst/extdata/ABC_list_char.rda
ENCODExplorer/inst/extdata/ABC_subset.rda
ENCODExplorer/inst/extdata/BRCA.rda
ENCODExplorer/inst/extdata/a549_ref.rda
ENCODExplorer/inst/extdata/dataFrame_integer.rda
ENCODExplorer/inst/extdata/tables.RDA
ENCODExplorer/inst/extdata/test_encode_ds.rda
ENCODExplorer/inst/extdata/test_encode_exp.rda
ENCODExplorer/inst/extdata/test_mouse_donor_df.rda
ENCODExplorer/inst/extdata/test_rest_query_file.rda
ENCODExplorer/inst/extdata/test_rest_search_dataset.rda
ENCODExplorer/inst/extdata/test_rest_search_experiment.rda
ENCODExplorer/inst/extdata/test_rest_search_file.rda
ENCODExplorer/inst/extdata/test_small_encode_df.rda
ENCODExplorer/inst/extdata/unitTest_df.rda
ENCODExplorer/inst/shiny
ENCODExplorer/inst/shiny/server.R
ENCODExplorer/inst/shiny/ui.R
ENCODExplorer/inst/unitTests
ENCODExplorer/inst/unitTests/Makefile
ENCODExplorer/inst/unitTests/local_test_clean_table.R
ENCODExplorer/inst/unitTests/local_test_extract_table.R
ENCODExplorer/inst/unitTests/local_test_getDatasetDetails.R
ENCODExplorer/inst/unitTests/local_test_getExperimentDetails.R
ENCODExplorer/inst/unitTests/local_test_getFileDetails.R
ENCODExplorer/inst/unitTests/local_test_getFileId.R
ENCODExplorer/inst/unitTests/local_test_query_transform.R
ENCODExplorer/inst/unitTests/test_clean_column.R
ENCODExplorer/inst/unitTests/test_createDesign.R
ENCODExplorer/inst/unitTests/test_download.R
ENCODExplorer/inst/unitTests/test_fuzzySearch.R
ENCODExplorer/inst/unitTests/test_query.R
ENCODExplorer/inst/unitTests/test_search.R
ENCODExplorer/man
ENCODExplorer/man/ENCODExplorer.Rd
ENCODExplorer/man/accession_df.Rd
ENCODExplorer/man/clean_column.Rd
ENCODExplorer/man/clean_table.Rd
ENCODExplorer/man/createDesign.Rd
ENCODExplorer/man/downloadEncode.Rd
ENCODExplorer/man/encode_df.Rd
ENCODExplorer/man/export_ENCODEdb_matrix.Rd
ENCODExplorer/man/extract_table.Rd
ENCODExplorer/man/fuzzySearch.Rd
ENCODExplorer/man/get_encode_types.Rd
ENCODExplorer/man/get_schemas.Rd
ENCODExplorer/man/prepare_ENCODEdb.Rd
ENCODExplorer/man/queryEncode.Rd
ENCODExplorer/man/searchEncode.Rd
ENCODExplorer/man/searchToquery.Rd
ENCODExplorer/tests
ENCODExplorer/tests/runTests.R
ENCODExplorer/vignettes
ENCODExplorer/vignettes/DBmodel.Rmd
ENCODExplorer/vignettes/DataUpdate.Rmd
ENCODExplorer/vignettes/ENCODExplorer.Rmd
ENCODExplorer/vignettes/img
ENCODExplorer/vignettes/img/model.png
ENCODExplorer/vignettes/img/query_mcf7.png
ENCODExplorer/vignettes/img/search_a549.png
ENCODExplorer/vignettes/img/shiny1.png
ENCODExplorer/vignettes/img/shiny2.png
ENCODExplorer/vignettes/img/wideDesign.png