Managing data from large scale projects such as The Cancer Genome Atlas (TCGA) for further analysis is an important and time consuming step for research projects. Several efforts, such as Firehose project, make TCGA pre-processed data publicly available via web services and data portals but it requires managing, downloading and preparing the data for following steps. We developed an open source and extensible R based data client for Firehose pre-processed data and demonstrated its use with sample case studies. Results showed that RTCGAToolbox could improve data management for researchers who are interested with TCGA data. In addition, it can be integrated with other analysis pipelines for following data analysis.
|Author||Mehmet Kemal Samur|
|Date of publication||2014-06-03 21:09:46|
|Maintainer||Mehmet Kemal Samur <firstname.lastname@example.org>|
|License||GPL (>= 2)|
CorResult-class: Class '"CorResult"'
DGEResult-class: Class '"DGEResult"'
FirehoseCGHArray-class: Class '"FirehoseCGHArray"'
FirehoseData-class: Class '"FirehoseData"'
FirehoseGISTIC-class: Class '"FirehoseGISTIC"'
FirehoseMethylationArray-class: Class '"FirehoseMethylationArray"'
FirehosemRNAArray-class: Class '"FirehosemRNAArray"'
getCNGECorrelation: Correlation between copy number data and gene expression...
getDiffExpressedGenes: Get differentially expressed genes between tumor and normal...
getFirehoseAnalyzeDates: Firehose data analyze run dates
getFirehoseData: Firehose project data client
getFirehoseDatasets: Get valid dataset alias.
getFirehoseRunningDates: Get valid analysis dates.
getMutationRate: Calculates the mutation ratio among the samples.
getReport: Make report plot.
getSurvival: Survival analysis based on gene expression value.
hg19.ucsc.gene.locations: hg19 known gene symbol and locations
RTCGASample: Sample TCGA Firehose data from BRCA dataset.
RTCGAToolbox-package: RTCGAToolbox: A data client and basic analysis toolbox for...