# Access matrix-like HDF5 server content or BigQuery content through a SummarizedExperiment interface

## Documentation for package ‘restfulSE’ version 1.2.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

.RESTfulSummarizedExperiment | Construct RESTfulSummarizedExperiment
assay | Construct RESTfulSummarizedExperiment
assay-method | Construct RESTfulSummarizedExperiment
assay-method | extract assay data
assayNames-method | HDF5Server-based assay for SummarizedExperiment
assayNames-method | Placeholder for assay name extractor for a BQSummarizedExperiment instance.
assays-method | Assays access for RESTfulSummarizedExperiment
BQ3_Array | create BQ3_Array instance given url (filepath) and entity (host) name
BQ3_Array-class | extension of DelayedArray for BigQuery content
BQ3_ArraySeed-class | BQ3_Array for BigQuery matrix content
BQ3_Matrix-class | extension of DelayedMatrix for HDF Server content
BQ3_Source | construct a BigQuery resource interface
BQ3_Source-class | Represent information about a BigQuery resource with a 'triple' database schema. This is targeting the isb-cgc TCGA layout. BigQuery Records are regarded as triples, within major groups defined by filtervbl. Triples have content subject - gene - value, to be pivoted to genes(rows) x subjects(columns) with values as entries.
bqConn | generate a connection to BigQuery for specific dataset
BQM_Array | create BQM_Array instance given url (filepath) and entity (host) name
BQM_Array-class | extension of DelayedArray for BigQuery content
BQM_ArraySeed-class | BQM_Array for BigQuery matrix content
BQM_Matrix-class | extension of DelayedMatrix for HDF Server content
BQM_Source | construct a BigQuery resource interface, for a matrix-like table with one column devoted to row identification (rowkeyfield) and all other columns assumed numeric
BQM_Source-class | Represent information about a BigQuery resource with a 'triple' database schema. This is targeting the isb-cgc TCGA layout. BigQuery Records are regarded as triples, within major groups defined by filtervbl. Triples have content subject - gene - value, to be pivoted to genes(rows) x subjects(columns) with values as entries.
BQSummarizedExperiment-class | Define a class to use BigQuery data through SummarizedExperiment interface
cgcConn | Simplify connection to a BigQuery dataset for the project "isb-cgc"
dim-method | dim derived from saved dimnames
dim-method | dim derived from saved dimnames
dim-method | Dimension access for RESTfulSummarizedExperiment
dimnames-method | dimnames are saved in the BQ3_ArraySeed
dimnames-method | dimnames are saved in the BQM_ArraySeed
goPatt | Create a data.frame with ENSEMBL and SYMBOL identifiers associated with a GO TERM specified by a regular expression in 'termPattern'
gtexTiss | Convenience function for access to gene-level GTEx tissues, as quantified in recount
isbCgcDatasets | Access the dataset names in the "isb-cgc" project
isbCgcTables | List the tables in a selected dataset
pancan_SE | illustrate DelayedArray assay from BigQuery backend in SummarizedExperiment
RESTfulSummarizedExperiment | Construct RESTfulSummarizedExperiment
RESTfulSummarizedExperiment-class | HDF5Server-based assay for SummarizedExperiment
RESTfulSummarizedExperiment-method | Construct RESTfulSummarizedExperiment
se1.3M | Convenience functions using EC2 server to extract tenx neurons full or subset data
se100k | Convenience functions using EC2 server to extract tenx neurons full or subset data
seByTumor | Given a BigQueryConnection to the 2017 GDC-oriented ISB TCGA bigtables, obtain a SummarizedExperiment 'shell' rowData and colData
seByTumor_2016 | Given a BigQueryConnection to the 2016 ISB TCGA bigtables, obtain a SummarizedExperiment 'shell' rowData and colData
tasicCortex | A set of mouse cortex marker genes.
[-method | HDF5Server-based assay for SummarizedExperiment