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FireBrowse Home

1.1.6 beta (2015_05_15)

  1. FeatureTable api: fixed GDAC-2988 (selecting columns was causing exception, reported by M. Deng)
  2. SMG api : changed the default to sort by rank instead of q value
  3. Initiated this release notes page, visible from the FireBrowse home.

1.1.5 beta (2015_05_11)

  1. Incorporated Spring 2015 Firehose Analysis run: over 8000 additional aliquots analyzed; added 7 new analysis tasks and over 300 analysis reports (nearly 1500 total).

  2. iCoMut: a powerful new synoptic tool for interpretation and exploration  CoMut figures have quickly become a staple of TCGA research. Within a single graphic they provide a comprehensive analysis profile, enabling the reader to quickly infer relationships between co-occurring results. With iCoMut researchers can now explore coMut figures interactively, sorting and reordering samples and results as they see fit.
  3. New viewGene expression visualizer: built on top of the FireBrowse RESTful APIviewGene generates a boxplot of mRNASeq expression levels for a selected gene across all cohorts.
  4. The fbget suite of automatically-generated, open source wrappers to the FireBrowse RESTful API.  fbget makes it even easier to ask both coarse- and fine-grained questions about TCGA data and Firehose analyses, from Python and the UNIX command line.

  5. Reports and FeatureTable apis now make older results available, too, not merely those from the latest analysis run. The search criterion is YYYY_MM_DD datestamp.
  6. We are also very happy to mention FireBrowseR, a set of open source R bindings to FireBrowse developed by a computer science Ph.D. student in Germany!

1.1.4 beta (2015_04_23)

  1. Loaded with Spring 2015 Firehose StandardData Run run
  2. Rationalized "requiredness" to be consistent across entire API: 
    1. Now, nearly all functions require that at least one gene OR cohort OR barcode be specified
    2. This increases query performance, and clarifies API semantics
  3. New Quartiles API for mRNASeq expression, providing a summary of expression across all samples in a disease cohort, suitable e.g. for boxplot visualization
  4. Corrected docs for SampleTypeBarcode function to indicate that it takes only 1 barcode (as a "path parameter")
  5. Changes to the default sort parameter for several API functions:
    1. mRNASeq api and miRSeq functions now default to disease cohort instead of gene and mir, respectively
    2. significantly mutated genes and mutation file functions now default to disease cohort instead of Q value and gene, respectively
  6. When iterating over multiple pages of TSV, CSV output, the api will now return a header for ONLY the first page
  7. Columns containing commas are now delimited with double quotes in CSV return payloads
  8. Increased tolerance for messy input: distinct values of multi-valued parameters (e.g. gene=egfr,tp53,BRCA1 in mRNASeq samples api) may now be delimited by arbitrary whitespace (in addition to commas, as previously supported)
  9. In the interactive docs UI the page and page_size parameters are no longer required by any API function: they continue to default to reasonable values for the common case.
  10. The payload of the SampleTypes api now returns the description of the sample type (e.g. TP = tumor primary)
  11. An empty response is now returned when no records in FireBrowse match a given query; previously a payload such as

     

    {
    "mRNASeq": []
    }

           would be returned in such cases (e.g. for this mRNASeq query).

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