Zodiac – Depiction of Genetic Interactions in Cancer by integrating TCGA data

Zodiac

:: 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

Yuan Ji Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: 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.

TCGA-Assembler 2.0.6 – Open-Source Software for Retrieving and Processing TCGA Data

TCGA-Assembler 2.0.6

:: 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

Yuan Ji Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R package

:: DOWNLOAD

 TCGA-Assembler

 :: 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.

RTCGAToolbox 2.21.5 – Exporting TCGA Firehose Data

RTCGAToolbox 2.21.5

:: 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

Mehmet Kemal Samur

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

RTCGAToolbox 

:: 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.

TCGA2STAT 1.2 – Simple TCGA Data Access for Integrated Statistical Analysis in R

TCGA2STAT 1.2

:: 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

  • Linux / windows/ MacOsX
  • R

:: DOWNLOAD

 TCGA2STAT

:: 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.