Man pages for mariodeng/FirebrowseR
An 'API' Client for Broads 'Firehose' Pipeline
| Analyses.CopyNumber.Genes.All | Retrieve all data by genes Gistic2 results. |
| Analyses.CopyNumber.Genes.Amplified | Retrieve Gistic2 significantly amplified genes results. |
| Analyses.CopyNumber.Genes.Deleted | Retrieve Gistic2 significantly deleted genes results. |
| Analyses.CopyNumber.Genes.Focal | Retrieve focal data by genes Gistic2 results. |
| Analyses.CopyNumber.Genes.Thresholded | Retrieve all thresholded by genes Gistic2 results. |
| Analyses.FeatureTable | Retrieve aggregated analysis features table. |
| Analyses.mRNASeq.Quartiles | Returns RNASeq expression quartiles, e.g. suitable for... |
| Analyses.Mutation.MAF | Retrieve MutSig final analysis MAF. |
| Analyses.Mutation.SMG | Retrieve Significantly Mutated Genes (SMG). |
| Analyses.Reports | Retrieve links to summary reports from Firehose analysis... |
| API.Version | Return the API version this package was build for |
| Archives.StandardData | Retrieve standard data archives. |
| Metadata.Centers | Obtain identities of TCGA consortium member centers. |
| Metadata.ClinicalNames | Retrieve names of all TCGA clinical data elements (CDEs). |
| Metadata.ClinicalNames_FH | Retrieve names of CDEs normalized by Firehose and selected... |
| Metadata.Cohort | Retrieve formal disease name(s) for cohort abbreviation(s). |
| Metadata.Cohorts | Translate TCGA cohort abbreviations to full disease names. |
| Metadata.Counts | Retrieve sample counts. |
| Metadata.Dates | Retrieve datestamps of all GDAC Firehose standard data and... |
| Metadata.HeartBeat | Simple way to discern whether API server is up and running |
| Metadata.MAFColNames | Retrieve names of all columns in the mutation annotation... |
| Metadata.Patients | Retrieve list of all TCGA patients. |
| Metadata.Platforms | Translate TCGA platform codes to full platform names. |
| Metadata.SampleType.Barcode | Given a TCGA barcode, return its short letter sample type... |
| Metadata.SampleType.Code | Translate from numeric to symbolic TCGA sample codes. |
| Metadata.SampleTypes | Return all TCGA sample type codes, both numeric and symbolic. |
| Metadata.SampleType.ShortLetterCode | Translate from symbolic to numeric TCGA sample codes. |
| Metadata.TSSites | Obtain identities of tissue source sites in TCGA. |
| Samples.Clinical | Retrieve TCGA CDEs verbatim, i.e. not normalized by Firehose. |
| Samples.Clinical_FH | Retrieve CDEs normalized by Firehose and selected for... |
| Samples.miRSeq | Retrieve miRSeq data. |
| Samples.mRNASeq | Retrieve mRNASeq data. |
