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| addsyms | add gene symbols to a GRanges that uses ensembl identifiers |
| basicColData | basicColData: metadata about a small collection of files for demonstrating TxRegInfra |
| basicFormatter | operate on a character vector to derive a DataFrame, splitting on a tokenand retrieving first and last split fragments as 'base' and 'type' fields |
| demo_eQTL_granges | a GRanges instance with eQTL metadata returned by 'sbov' |
| demo_fimo_granges | a list of GRanges instances with TF FIMO scores returned by 'fimo_granges' |
| dgf_meta | dgf_meta: metadata about a small collection of bed files for demonstrating TxRegInfra |
| dnmeta | metadata about DNaseI hotspots from ENCODE |
| dnmetaApp | support search of hotspot/peak data from ENCODE |
| getDocumentFields | determine the fields present in a txregnet document |
| getFieldNames | get names of fields in a collection in remote txregnet |
| grConverter | convert a GRanges to a JSON query for mongodb |
| importBedToMongo | arrange import to mongo using mongoimport, setting up type and fields appropriately |
| listAllCollections | list all collections in a database, using command-line interface |
| makeAggregator | generate JSON to aggregate (counting records, and, by default, averaging a given variable) within a collection |
| makeColData | generate a colData component corresponding to a mongodb |
| makeGRConverterList | generate a list of GRanges to JSON for queries to mongo |
| oldbasicColData | oldbasicColData: metadata about a small collection of files for demonstrating TxRegInfra |
| ragged41FP | ragged41FP: A RaggedExperiment instance with digital genomic footprints over the coding region of ORMDL3 |
| RaggedMongoExpt | bind colData to a mongo-based ragged-experiment incubator |
| sbov | prototype of subsetter for mongo resource |
| sbov_output_eQTL | a GRanges instance with eQTL metadata returned by 'sbov' |
| sbov_output_FP | a GRanges instance with digital genomic footprint metadata returned by 'sbov' |
| sbov_output_HS | a GRanges instance with DnaseI hotspot metadata returned by 'sbov' |
| sbov_to_graphNEL | convert sbov() output to annotated graphNEL |
| txmodels | use Gviz to render transcript models via GeneRegionTrack, but keep lightweight through requireNamespace and suggestion for installation |
| txregCollections | list collections in AWS mongo server for txregnet |
| URL_txregInAWS | return mongodb URL for working mongo server |
| URL_txregLocal | local mongodb txregnet |
| verifyHasMongoCmd | check for existence of 'mongo' command, for db.getCollectionNames etc. |
| verifyRunningMongodb | check for accessible local mongodb |