:: DESCRIPTION
TCGA2STAT automatically downloads and processes TCGA genomics and clinical data into a format convenient for statistical analyses in the R environment.
:: DEVELOPER
Liu Lab, Baylor College of Medicine
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
TCGA2STAT: Simple TCGA Data Access for Integrated Statistical Analysis in R.
Wan YW, Allen GI, Liu Z.
Bioinformatics. 2015 Nov 14. pii: btv677.
:: DESCRIPTION
Zodiac is a computational tool and resource to integrate existing knowledge about cancer genetic interactions with new information contained in TCGA data. It is an evolution of existing knowledge by treating it as a prior graph, integrating it with a likelihood model derived by Bayesian graphical model based on TCGA data, and producing a posterior graph as updated and data-enhanced knowledge. In short, Zodiac realizes “Prior interaction map + TCGA data → Posterior interaction map.”
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhu Y, Xu Y, Helseth DL Jr, Gulukota K, Yang S, Pesce LL, Mitra R, Müller P, Sengupta S, Guo W, Silverstein JC, Foster I, Parsad N, White KP, Ji Y.
Zodiac: A Comprehensive Depiction of Genetic Interactions in Cancer by Integrating TCGA Data.
J Natl Cancer Inst. 2015 May 8;107(8):djv129. doi: 10.1093/jnci/djv129. PMID: 25956356; PMCID: PMC4554190.
:: DESCRIPTION
TCGA-Assembler is an open-source, freely available tool that automatically downloads, assembles, and processes public The Cancer Genome Atlas (TCGA) data, to facilitate downstream data analysis by relieving investigators from the burdens of data preparation.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
TCGA-Assembler: Open-Source Software for Retrieving and Processing TCGA Data
Yitan Zhu, Peng Qiu, Yuan Ji*
Nat Methods. 2014 Jun;11(6):599-600. doi: 10.1038/nmeth.2956.
:: DESCRIPTION
RTCGAToolbox is 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 further data analysis.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Samur MK.
RTCGAToolbox: a new tool for exporting TCGA Firehose data.
PLoS One. 2014 Sep 2;9(9):e106397. doi: 10.1371/journal.pone.0106397. PMID: 25181531; PMCID: PMC4152273.
