1.1.15 beta (2015_08_24)
- Added Code, CenterType, and ShortName fields to the payload returned by the Metadata/Centers api function
- The HeartBeat function now returns the version number and build time/date, too
- Re-ingested data served by Clinical samples function, to filter non-ASCII characters
- To address this viewGene issue, insert gene name into metadata to ensure cache is suitably invalidated.
- Addressed a performance issue that had crept into the FireBrowse landing page: the sample counts barchart was noticeably slow to load, apparently since mid-August due to a typo in the font name. Strangely, the typo has been there all along, but the landing page has only been slow for about 1 week. It is fast again.
1.1.14 beta (2015_07_23)
- Fixed the
download_dialog feature of the landing page, so that data browsing redirects from the GDAC homepage once again pop up dialogs resembling this:
- Updated the Clinical samples API to reference the new interactive CDE table, which on a single page shows exactly what CDEs are available for all disease cohorts.
1.1.13 beta (2015_07_10)
viewGene now has a cohort filter control, allowing subsets of cohorts to be viewed:
iCoMut now properly shows LAML data; and includes a few other small fixes
- Updated the online tutorial.
1.1.12 beta (2015_06_29)
Enable password protection when displaying (unpublished) analysis working group (AWG) results
1.1.11 beta (2015_06_24)
- Updated to reflect June 2015 stddata run.
- fbget Python and UNIX cli bindings updated to v0.1.4, and now also installable from PyPi via the pip tool.
1.1.10 beta (2015_06_09)
- New control added to viewGene, enabling it to visualize RPKM format expression data; as some cohorts (e.g. ESCA, STAD, STES) do not have RSEM expression data.
1.1.9 beta (2015_06_04)
- Internal modifications to simplify deployment
1.1.8 beta (2015_06_01)
- Remove scale control from viewGene widget
1.1.7 beta (2015_05_18)
- Make rawMAF datatype visible in user interface and API
1.1.6 beta (2015_05_15)
- FeatureTable api: fixed GDAC-2988 (selecting columns was causing exception, reported by M. Deng)
- SMG api : changed the default to sort by rank instead of q value
- Initiated this release notes page, visible from the FireBrowse home
1.1.5 beta (2015_05_11)
Incorporated Spring 2015 Firehose Analysis run: over 8000 additional aliquots analyzed; added 7 new analysis tasks and over 300 analysis reports (nearly 1500 total)
- 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.
- New viewGene expression visualizer: built on top of the FireBrowse RESTful API,
viewGene generates a boxplot of mRNASeq expression levels for a selected gene across all cohorts.
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.
- 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.
- 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)
- Loaded with Spring 2015 Firehose StandardData Run run
- Rationalized "requiredness" to be consistent across entire API:
- Now, nearly all functions require that at least one gene OR cohort OR barcode be specified
- This increases query performance, and clarifies API semantics
- New Quartiles API for mRNASeq expression, providing a summary of expression across all samples in a disease cohort, suitable e.g. for boxplot visualization
- Corrected docs for SampleTypeBarcode function to indicate that it takes only 1 barcode (as a "path parameter")
- Changes to the default sort parameter for several API functions:
- mRNASeq api and miRSeq functions now default to disease cohort instead of gene and mir, respectively
- significantly mutated genes and mutation file functions now default to disease cohort instead of Q value and gene, respectively
- When iterating over multiple pages of TSV, CSV output, the api will now return a header for ONLY the first page
- Columns containing commas are now delimited with double quotes in CSV return payloads
- 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)
- 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.
- The payload of the SampleTypes api now returns the description of the sample type (e.g. TP = tumor primary)
An empty response is now returned when no records in FireBrowse match a given query; previously a payload such as
would be returned in such cases (e.g. for this mRNASeq query).