RTCGA-package
(Package: RTCGA) :
The Caner Genome Atlas data integration
The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high level sequence analysis of the tumor genomes. The key is to understand genomics to improve cancer care. RTCGA package offers download and integration of the variety and volume of TCGA data using patient barcode key, what enables easier data possession. This may have an benefcial infuence on impact on development of science and improvement of patients' treatment. Furthermore, RTCGA package transforms TCGA data to form which is convenient to use in R statistical package. Those data transformations can be a part of statistical analysis pipeline which can be more reproducible with RTCGA
● Data Source:
BioConductor
● Keywords:
● Alias: RTCGA, RTCGA-package
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boxplotTCGA
(Package: RTCGA) :
Create Boxplots for TCGA Datasets
Function creates boxplots (geom_boxplot) for TCGA Datasets.
● Data Source:
BioConductor
● Keywords:
● Alias: boxplotTCGA
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9 images
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checkTCGA
(Package: RTCGA) :
Information about datasets from TCGA project
The checkTCGA function let's to check
● Data Source:
BioConductor
● Keywords:
● Alias: checkTCGA
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convertTCGA
(Package: RTCGA) :
Convert data from RTCGA family to Bioconductor classes
Functions use Biobase (http://bioconductor.org/packages/release/bioc/html/Biobase.html) package to transform data from packages from RTCGA data family to Bioconductor classes (RTCGA.rnaseq, RTCGA.RPPA, RTCGA.PANCAN12, mRNA, RTCGA.methylation to ExpressionSet and RTCGA.CNV to GRanges). For RTCGA.PANCAN12 there is sense to convert expression.cb1, expression.cb2, cnv.cb .
● Data Source:
BioConductor
● Keywords:
● Alias: convertPANCAN12, convertTCGA
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datasetsTCGA
(Package: RTCGA) :
RTCGA.data - The Family of R Packages with Data from The Cancer Genome Atlas Study
Snapshots of the clinical, mutations, CNVs, rnaseq, RPPA, mRNA, miRNASeq and methylation datasets from the 2015-11-01 release date (check all dates of release with checkTCGA('Dates') ) are included in the RTCGA.data family (factory) that contains 9 packages:
● Data Source:
BioConductor
● Keywords:
● Alias: datasetsTCGA
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Enables to download TCGA data from specified dates of releases of concrete Cohorts of cancer types. Pass a name of required dataset to the dataSet parameter. By default the Merged Clinical dataSet is downloaded (value dataSet = 'Merge_Clinical.Level_1' ) from the newest available date of the release.
● Data Source:
BioConductor
● Keywords:
● Alias: downloadTCGA
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expressionsTCGA
(Package: RTCGA) :
Gather Expressions for TCGA Datasets
Function gathers expressions over multiple TCGA datasets and extracts expressions for desired genes. See rnaseq, mRNA, RPPA, miRNASeq, methylation.
● Data Source:
BioConductor
● Keywords:
● Alias: expressionsTCGA
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heatmapTCGA
(Package: RTCGA) :
Create Heatmaps for TCGA Datasets
Function creates heatmaps (geom_tile) for TCGA Datasets.
● Data Source:
BioConductor
● Keywords:
● Alias: heatmapTCGA
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4 images
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infoTCGA
(Package: RTCGA) :
Information about cohorts from TCGA project
Function restores codes and counts for each cohort from TCGA project.
● Data Source:
BioConductor
● Keywords:
● Alias: infoTCGA
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installTCGA
(Package: RTCGA) :
Install packages from RTCGA family
Function installs data packages from https://github.com/RTCGA/. Packages are listed datasetsTCGA.
● Data Source:
BioConductor
● Keywords:
● Alias: installTCGA
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