Tag: Cancer

DriverNet 1.0.0 – Predict Functional Important Driver Genes in Cancer Genome

DriverNet 1.0.0

:: DESCRIPTION

DriverNet is a package to predict functional important driver genes in cancer by integrating genome data (mutation and copy number variation data) and transcriptome data (gene expression data). The different kinds of data are combined by an influence graph, which is a gene-gene interaction network deduced from pathway data. A greedy algorithm is used to find the possible driver genes, which may mutated in a larger number of patients and these mutations will push the gene expression values of the connected genes to some extreme values.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R package

:: DOWNLOAD

  DriverNet

:: MORE INFORMATION

Citation

Genome Biol. 2012 Dec 22;13(12):R124.
DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.
Bashashati A, Haffari G, Ding J, Ha G, Lui K, Rosner J, Huntsman DG, Caldas C, Aparicio SA, Shah SP.

CopyNumber450kCancer 1.0.4 – Baseline Correction for Copy Number Data from Cancer Samples

CopyNumber450kCancer 1.0.4

:: DESCRIPTION

CopyNumber450kCancer takes the output of CopyNumber450k and ChAMP packages and correct the baseline in each sample for accurate copy number calling, specially in cancer samples. CopyNumber450kCancer can read the segment output file from CopyNumber450k package directly without any need for modification. Output files from ChAMP need to be in one file not in seperated files.

::DEVELOPER

Molecular Medicine research group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

 CopyNumber450kCancer

:: MORE INFORMATION

Citation

CopyNumber450kCancer: Baseline Correction for Accurate Copy Number Calling from the 450k Methylation Array.
Marzouka NA, Nordlund J, Bäcklin CL, Lönnerholm G, Syvänen AC, Almlöf JC.
Bioinformatics. 2015 Nov 9. pii: btv652

Statius – Prediction of Individualized Therapeutic Vulnerabilities in Cancer from Genomic Profiles

Statius

:: DESCRIPTION

Statius is a web-based tool prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles

::DEVELOPER

Computational Biology Center @ Memorial Sloan Kettering Cancer Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles.
Aksoy BA, Demir E, Babur Ö, Wang W, Jing X, Schultz N, Sander C.
Bioinformatics. 2014 Jul 15;30(14):2051-9. doi: 10.1093/bioinformatics/btu164.

PPISURV – Cancer Survival Analyses

PPISURV

:: DESCRIPTION

PPISURV is a novel bioinformatics tool for uncovering the hidden role of specific genes in cancer survival outcome

::DEVELOPER

PPISURV team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PPISURV: a novel bioinformatics tool for uncovering the hidden role of specific genes in cancer survival outcome.
Antonov AV, Krestyaninova M, Knight RA, Rodchenkov I, Melino G, Barlev NA.
Oncogene . 2014 Mar 27;33(13):1621-8. PMID:23686313

OpenCRAVAT 2.2.7 – Open Custom Ranked Analysis of Variants Toolkit

OpenCRAVAT 2.2.7

:: DESCRIPTION

OpenCRAVAT is a new open source, scalable decision support system to support variant and gene prioritization. It offers a dynamic GUI, allowing users to easily, download tools from an extensive resource catalog, create customized pipelines, run jobs at speeds that exceed current variant annotation API services, and explore results in a richly detailed viewing environment.

::DEVELOPER

Karchin Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/ Linux

:: DOWNLOAD

OpenCRAVAT

:: MORE INFORMATION

Citation

Pagel KA, Kim R, Moad K, Busby B, Zheng L, Tokheim C, Ryan M, Karchin R.
Integrated Informatics Analysis of Cancer-Related Variants.
JCO Clin Cancer Inform. 2020 Mar;4:310-317. doi: 10.1200/CCI.19.00132. PMID: 32228266; PMCID: PMC7113103.

CRAVAT: cancer-related analysis of variants toolkit.
Douville C, Carter H, Kim R, Niknafs N, Diekhans M, Stenson PD, Cooper DN, Ryan M, Karchin R.
Bioinformatics. 2013 Mar 1;29(5):647-8. doi: 10.1093/bioinformatics/btt017. Epub 2013 Jan 16.

CNAnorm 1.39.0 – Estimate Copy Number Aberrations (CNA) in Cancer Samples

CNAnorm 1.39.0

:: DESCRIPTION

CNAnorm is an R package to perform normalisation of copy number from next generation sequence data, taking into account tumour cell content and possible aneuploid genome size.

::DEVELOPER

the LICP Pre-Cancer Genomics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • R package
  • Bioconductor

:: DOWNLOAD

 CNAnorm

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jan 1;28(1):40-7. doi: 10.1093/bioinformatics/btr593. Epub 2011 Oct 28.
Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data.
Gusnanto A, Wood HM, Pawitan Y, Rabbitts P, Berri S.

SomatiCA 1.12.0 – Analysis of Somatic CNAs from Cancer Genome Sequencing

SomatiCA 1.12.0

:: DESCRIPTION

SomatiCA is a computational framework which explicitly accounts for tumor purity and subclonality in the analysis of somatic copy-number profiles.

::DEVELOPER

Chen Group at U Chicago

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • R 
  • BioConductor

:: DOWNLOAD

SomatiCA

:: MORE INFORMATION

Citation

PLoS One. 2013 Nov 12;8(11):e78143. doi: 10.1371/journal.pone.0078143. eCollection 2013.
SomatiCA: identifying, characterizing and quantifying somatic copy number aberrations from cancer genome sequencing data.
Chen M1, Gunel M, Zhao H.

tsRFun – A Web Server to Detect tRFs and their expression in multiple Cancers

tsRFun

:: DESCRIPTION

tsRFun provides multiple tools for a real-time online tsRNA identification, tsRNA target prediction, and functional enrichment analysis. In summary, tsRFun provides an effective data resource and analysis tool for studying the function and role of tsRNA in cancer.

::DEVELOPER

tsRFun team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

tRF2Cancer: A web server to detect tRNA-derived small RNA fragments (tRFs) and their expression in multiple cancers.
Zheng LL, Xu WL, Liu S, Sun WJ, Li JH, Wu J, Yang JH, Qu LH.
Nucleic Acids Res. 2016 May 13. pii: gkw414.

CONEXIC – COpy Number and EXpression In Cancer

CONEXIC

:: DESCRIPTION

CONEXIC is an algorithm that integrates matched copy number (amplifications and deletions) and gene expression data from tumor samples to identify driving mutations and the processes they influence.

::DEVELOPER

Dana Pe’er Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

 CONEXIC

:: MORE INFORMATION

Citation

Cell. 2010 Dec 10;143(6):1005-17. doi: 10.1016/j.cell.2010.11.013. Epub 2010 Dec 2.
An integrated approach to uncover drivers of cancer.
Akavia UD, Litvin O, Kim J, Sanchez-Garcia F, Kotliar D, Causton HC, Pochanard P, Mozes E, Garraway LA, Pe’er D.

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