# TCGAutils ------------------------------------------------------------ ## Changes in version 0.99.68 ### Minor changes and bug fixes * Minor changes in response to review, avoid switching from logical to numeric index, updated vignette introduction * Fix examples to updated `GenomicDataCommons` interface * Move `RTCGAToolbox` to `Suggests` field in DESCRIPTION * Removed `BiocFileCache` from `Imports` field ## Changes in version 0.99.51 ### New features * Added a group of ID translation helper functions (see ?ID-translation) * Added a group of helper functions that work with `curatedTCGAData` * `UUIDtoBarcode` function added thanks to @seandavi * Renamed `makeGRangesListFromTCGA` to `makeGRangesListFromCopyNumber` * `makeSummarizedExperimentFromGISTIC` is now available to convert `RTCGAToolbox`'s `FirehoseGISTIC` data class to `SummarizedExperiment` * Created a function to merge external `colData` to a `MultiAssayExperiment` `colData` slot * Revamped vignette documentation ### Minor changes and bug fixes * Improvements to `TCGAbiospec` and `TCGAbarcode` * Updated `sampleTypes` and `clinicalNames` datasets * Updated DESCRIPTION file with appropriate imports and exports * Various improvements to `findGRangesCols` * `generateMap` is now updated to the recent `MultiAssayExperiment` API with improved example * Updated `getFileNames` to most recent `RTCGAToolbox` API * Various updates to data generating scripts in `data-raw` folder * Format updates to NEWS file * Added tests ## Changes in version 0.2.0 ### New features * Package renamed to `TCGAutils` for working with TCGA data ## Changes in version 0.1.0 ### New features * `TCGAtranslateID` now works with GDC API ### Minor changes and bug fixes * Code cleaned up * Added proper import directives ## Changes in version 0.0.70 ### New features * `makeGRangesListFromDataFrame` now moved to `GenomicRanges` * `makeSummarizedExperimentFromDataFrame` now moved to `SummarizedExperiment` * `getFileNames` function will obtain filenames used in `RTCGAToolbox` * Improved `getFileNames` with `xml2` and `rvest` dependencies and removes the `XML` dependency ### Minor changes and bug fixes * `TCGAextract` now uses the `findGRangesCols` to automatically detect ranged data columns * Arguments in functions `TCGA*` now renamed to match `MultiAssayExperiment` conventions * Informative errors in `TCGAextract` ## Changes in version 0.0.60 * `makeGRangesListFromTCGA` data builds on `makeGRangesListFromDataFrame` * `makeGRangesListFromDataFrame` and `makeRangedSummarizedExperimentFromDataFrame` will be moving to standard Bioconductor packages soon. * `tcga` and `ccle` functions soon to be deprecated. * Upcoming: `TCGAbarcode` will be modified for efficiency ## Changes in version 0.0.50 * Add your own identifier parsing function for generating a `sampleMap` in `generateMap`! * Add proper genome build to ranged based objects. * Return `SummarizedExperiment` class for certain data types. * Fix genome build bugs ## Changes in version 0.0.46 * `makeRSE` function for creating a `RangedSummarizedExperiment` object from a data frame. * Bug fixes to `getRangeNames` including the option to enter a regular expression vector for finding ranged column names. * `matchClinical` renamed to `TCGAmatchClinical` ## Changes in version 0.0.44 * `getRangedNames` function will try to extract minimum necessary names for creating ranges (works on a vector of names) * minor bug fixes to `TCGAbiospec`, `TCGAextract`, `makeGRangesList` ## Changes in version 0.0.40 * Package renamed to `BiocInterfaces`! * `TCGA` specific functions now start with the letters `TCGA` * Included: more examples of use of the `TCGAbarcode` function * Updated `makeGRangesList` function to work with `tcga` and `ccle` data parameter functions ## Changes in version 0.0.2 * Added a `NEWS.md` file to track changes to the package. * TCGAmisc now a standalone package! (previously in `RTCGAToolbox`) * Provides helper functions for converting raw data into S4 objects (e.g., `GRangesList`) * Provides functions for creating a MultiAssayExperiment object such as: * `generateTCGAmap` * `cleanExpList`