1.1.17 beta (2015_09_27)
- Ingest the August 2015 Firehose standard data run:
API through which Firehose-picked and normalized clinical data are accessible has been renamed to Samples/Clinical_FH
Verbatim TCGA clinical data may be accessed through the new Samples/Clincal API
A CDE will be reflected in either API only when it has a value other than NA for at least 1 patient case in any disease cohort.
- For backward compatibility, the Samples/ClinicalTier1 remains available (as a synonym for Samples/Clinical_FH)
- fbget Python and UNIX CLI bindings have been suitably updated
- Which makes it extremely easy to determine for what patients and cohorts any given CDE is defined: e.g.
fbget clinical cde=gleason_score
will show each patient case with a valid
gleason_score, across all cohorts
- viewGene: now enforces rendering of at most 1 gene per Submit; if multiple genes are given the first is selected
- Popup tooltips for mutation panels now show total # of mutations AND fractional % of a given type (e.g. missense)
- New search feature, enabling one to see into which clusters/panels/etc a given patient (or set of patients) falls
- After extensive testing, upgraded backend database from Mongo2.x to Mongo3.x: v3 dramatically reduces the memory footprint and data storage sizes, which yields greater performance and also clears considerable breathing room to add more data APIs (e.g. for methylation, RPPA, etc) as well as AWG-specific databases
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).