ENCODExplorer: A compilation of ENCODE metadata
Version 2.2.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorCharles Joly Beauparlant <charles.joly-beauparlant@crchul.ulaval.ca>, Audrey Lemacon <lemacon.audrey@ulaval.ca>, Louis Gendron <louisg.212@gmail.com> Astrid-Louise Deschenes, <astrid-louise.deschenes@crchudequebec.ulaval.ca> and Arnaud Droit <arnaud.droit@crchudequebec.ulaval.ca >
Bioconductor views DataImport Infrastructure
Date of publicationNone
MaintainerCharles Joly Beauparlant <charles.joly-beauparlant@crchul.ulaval.ca>
LicenseArtistic-2.0
Version2.2.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ENCODExplorer")

Man pages

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 used to download a serie of files or...
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.
shinyEncode: Launch a shiny interface for ENCODExplorer

Functions

ENCODExplorer Man page
ENCODExplorer-package Man page
clean_column Man page Source code
clean_table Man page Source code
createDesign Man page Source code
downloadEncode Man page Source code
download_dt_file Source code
download_single_file Source code
encode_df Man page
export_ENCODEdb_matrix Man page Source code
extract_table Man page Source code
fuzzySearch Man page Source code
get_encode_types Man page Source code
get_schemas Man page Source code
prepare_ENCODEdb Man page Source code
queryEncode Man page Source code
query_transform Source code
searchEncode Man page Source code
searchToquery Man page Source code
shinyEncode Man page Source code
step1 Source code
step10 Source code
step11 Source code
step2 Source code
step3 Source code
step4 Source code
step5 Source code
step6_assay Source code
step6_biosample_name Source code
step6_biosample_type Source code
step6_control Source code
step6_date_released Source code
step6_status Source code
step6_target Source code
step7 Source code
step8 Source code
step9 Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/ENCODExplorer.R
R/createDesign.R
R/download.R
R/fuzzySearch.R
R/prepare_data.R
R/query.R
R/rest_api.R
R/shiny_encode.R
README.md
build
build/vignette.rds
data
data/datalist
data/encode_df.rda
inst
inst/doc
inst/doc/DBmodel.R
inst/doc/DBmodel.Rmd
inst/doc/DBmodel.html
inst/doc/DataUpdate.R
inst/doc/DataUpdate.Rmd
inst/doc/DataUpdate.html
inst/doc/ENCODExplorer.R
inst/doc/ENCODExplorer.Rmd
inst/doc/ENCODExplorer.html
inst/extdata
inst/extdata/ABC_df_lab.rda
inst/extdata/ABC_list_char.rda
inst/extdata/ABC_subset.rda
inst/extdata/BRCA.rda
inst/extdata/a549_ref.rda
inst/extdata/dataFrame_integer.rda
inst/extdata/tables.RDA
inst/extdata/test_encode_ds.rda
inst/extdata/test_encode_exp.rda
inst/extdata/test_mouse_donor_df.rda
inst/extdata/test_rest_query_file.rda
inst/extdata/test_rest_search_dataset.rda
inst/extdata/test_rest_search_experiment.rda
inst/extdata/test_rest_search_file.rda
inst/extdata/test_small_encode_df.rda
inst/extdata/unitTest_df.rda
inst/shiny
inst/shiny/server.R
inst/shiny/ui.R
inst/unitTests
inst/unitTests/Makefile
inst/unitTests/local_test_clean_table.R
inst/unitTests/local_test_extract_table.R
inst/unitTests/local_test_getDatasetDetails.R
inst/unitTests/local_test_getExperimentDetails.R
inst/unitTests/local_test_getFileDetails.R
inst/unitTests/local_test_getFileId.R
inst/unitTests/local_test_query_transform.R
inst/unitTests/test_clean_column.R
inst/unitTests/test_createDesign.R
inst/unitTests/test_download.R
inst/unitTests/test_fuzzySearch.R
inst/unitTests/test_query.R
inst/unitTests/test_search.R
man
man/ENCODExplorer.Rd
man/clean_column.Rd
man/clean_table.Rd
man/createDesign.Rd
man/downloadEncode.Rd
man/encode_df.Rd
man/export_ENCODEdb_matrix.Rd
man/extract_table.Rd
man/fuzzySearch.Rd
man/get_encode_types.Rd
man/get_schemas.Rd
man/prepare_ENCODEdb.Rd
man/queryEncode.Rd
man/searchEncode.Rd
man/searchToquery.Rd
man/shinyEncode.Rd
tests
tests/runTests.R
vignettes
vignettes/DBmodel.Rmd
vignettes/DataUpdate.Rmd
vignettes/ENCODExplorer.Rmd
vignettes/img
vignettes/img/model.png
vignettes/img/query_mcf7.png
vignettes/img/search_a549.png
vignettes/img/shiny1.png
vignettes/img/shiny2.png
vignettes/img/wideDesign.png
ENCODExplorer documentation built on May 20, 2017, 9:20 p.m.