NEWS.md

In RTCGA/RTCGA: The Cancer Genome Atlas Data Integration

Version 1.27.2

• moved createTCGA() out of the package

Version 1.27.1

• Fixed http and https calls to https://gdac.broadinstitute.org/

Version 1.23.1

• Merged Bioconductor git repo with GitHub git repo

Version 1.7.1

• New version of RTCGA website - http://rtcga.github.io/RTCGA/, based on pkgdown
• Improved RTCGA workflow graph - https://raw.githubusercontent.com/RTCGA/RTCGA/master/RTCGA_workflow.png
• Added createTCGA function which can now create RTCGA.dataType.releaseDate-like data packages. Most of the function result will be published in ExperimentHub on Bioconductor.

• Check new data packages with datasets from 2016-01-28 release date from TCGA

  • https://github.com/RTCGA/RTCGA.clinical.20160128
  • https://github.com/RTCGA/RTCGA.mutations.20160128
  • https://github.com/RTCGA/RTCGA.rnaseq.20160128
  • https://github.com/RTCGA/RTCGA.RPPA.20160128
  • https://github.com/RTCGA/RTCGA.CNV.20160128
  • https://github.com/RTCGA/RTCGA.mRNA.20160128
  • https://github.com/RTCGA/RTCGA.miRNASeq.20160128
  • https://github.com/RTCGA/RTCGA.methylation.20160128

• readTCGA now has a method for CNV datasets.

• You can now download packages from .20160128 release with installTCGA function, which downloads them all by default.
• Improved documentation titles.
• Improved manual page of installTCGA after adding packages from 2016-01-08.
• Provided wider explanation for ?datasetsTCGA after adding packages from 2016-01-08.
• Extended biocViews.
• Shortened examples and improved their code appearance.
• Subsitute old URLs in manual pages with new ones - RTCGA website has new architecture.

Version 1.3.3

• Fixed examples in expressionsTCGA that broke after changes in dplyr, while moving to tibbles.

Version 1.1.15

• New functions heatmapTCGA, boxplotTCGA, kmTCGA, pcaTCGA, theme_RTCGA for plotting https://rtcga.github.io/RTCGA/Visualizations.html
• New functions mutationsTCGA, expressionsTCGA, survivalTCGA for data manipulations.
• New website https://rtcga.github.io/RTCGA/

Version 1.1

• New parameter allDataSets for downloadTCGA that allows to download all files matching string in the dataSet parameter.
• New documentation page ?datasetsTCGA.
• readTCGA has now new method for below files
  • RPPA (reverse phase protein array),
  • mRNA (Merge transcriptome agilent),
  • miRNASeq
  • methylation (methylation datasets)
• datasetsTCGA documentation has been extended with new datasets for rppa and mrna
• downloadTCGA now gives a warning when more than one file matches dataSet parameter, and downloads the first matched dataset without FFPE in the name. If all matching datasets have FFPE in the name then the first of them is downloaded.
• checkTCGA now downloads also sizes with datasets names when one specifies what parameter to DatSets.
• Updated tests for checkTCGA
• Added new installTCGA function that can install all packages from RTCGA family.
• Added new convertTCGA function that converts data.frames from RTCGA family to Bioconductor classes.
• New examples in readTCGA function documentation concerning the following datasets:
  • methylation
  • RPPA
  • mRNA
  • miRNASeq
  • isoforms

Version 1.0

functions - readTCGA - infoTCGA - checkTCGA - downloadTCGA

RTCGA/RTCGA documentation built on Nov. 1, 2022, 8:15 p.m.