shinyGEO – Identifying Biomarkers in Gene Expression Omnibus datasets

shinyGEO

:: DESCRIPTION

shinyGEO is a web-based application for performing differential expression and survival analysis on Gene Expression Omnibus datasets

::DEVELOPER

Bioinformatics Laboratory at Eastern Connecticut State University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

 shinyGEO

:: MORE INFORMATION

Citation

shinyGEO: a web-based application for analyzing Gene Expression Omnibus datasets.
Dumas J, Gargano MA, Dancik GM.
Bioinformatics. 2016 Aug 8. pii: btw519.

MIRUMIR – microRNA as Biomarker In Cancer

MIRUMIR

:: DESCRIPTION

MIRUMIR is an online tool to test microRNAs as biomarkers to predict survival in cancer using multiple clinical data sets.

::DEVELOPER

MIRUMIR team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

MIRUMIR: an online tool to test microRNAs as biomarkers to predict survival in cancer using multiple clinical data sets.
Antonov AV, Knight RA, Melino G, Barlev NA, Tsvetkov PO.
Cell Death Differ. 2013 Feb;20(2):367. doi: 10.1038/cdd.2012.137

PAA 1.4.1 – Biomarker Discovery with Protein Microarrays

PAA 1.4.1

:: DESCRIPTION

The R/Bioconductor package PAA (Protein Array Analyzer) facilitates a flexible analysis of protein microarrays for biomarker discovery (esp., ProtoArrays).

::DEVELOPER

Medizinisches Proteom-Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • R/ BioConductor

:: DOWNLOAD

 PAA

:: MORE INFORMATION

Citation

PAA: An R/Bioconductor package for biomarker discovery with protein microarrays.
Turewicz M, Ahrens M, May C, Marcus K, Eisenacher M.
Bioinformatics. 2016 Jan 22. pii: btw037

lodGWAS 1.0-7 – Genome-Wide Association Analysis of a Biomarker Accounting for Limit of Detection

lodGWAS 1.0-7

:: DESCRIPTION

lodGWAS is a software package for genome-wide association anal-ysis of biomarkers with a limit of detection.

::DEVELOPER

Ahmad Vaez, Ilja M. Nolte<i.m.nolte at umcg.nl>, Peter J. van der Most

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 lodGWAS

:: MORE INFORMATION

Citation

lodGWAS: a software package for genome-wide association anal-ysis of biomarkers with a limit of detection.
Vaez A, van der Most PJ, Prins BP, Snieder H, van den Heuvel E, Alizadeh BZ, Nolte IM.
Bioinformatics. 2016 Jan 22. pii: btw021

Biomarker – Biomarker Selection using Logit-Laplacian-net

Biomarker

:: DESCRIPTION

Biomarker uses graph Laplacian regularized logistic regression to integrate biological networks into disease classification and pathway association problems

:: DEVELOPER

Liu Lab, Baylor College of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / windows/ MacOsX
  • Matlab

:: DOWNLOAD

 Biomarker

:: MORE INFORMATION

Citation

BMC Genomics. 2013;14 Suppl 8:S7. doi: 10.1186/1471-2164-14-S8-S7. Epub 2013 Dec 9.
Molecular pathway identification using biological network-regularized logistic models.
Zhang W, Wan YW, Allen GI, Pang K, Anderson ML, Liu Z.

netClass – An R Package for Network-Based Biomarker Discovery

netClass 1.2.1

:: DESCRIPTION

netClass is an R package for network-based feature (gene) selection for biomarkers discovery via integrating biological information.

::DEVELOPER

ALGORITHMIC BIOINFORMATICS

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

  netClass

:: MORE INFORMATION

Citation

netClass: an R-package for network based, integrative biomarker signature discovery.
Cun Y, Fröhlich H.
Bioinformatics. 2014 May 1;30(9):1325-6. doi: 10.1093/bioinformatics/btu025.

omniBiomarker – Knowledge-Driven Biomarker Identification and Data Combination

omniBiomarker

:: DESCRIPTION

OmniBiomarker is a web-based bioinformatics application that addresses the microarray “curse of dimensionality” problem as well as the software standards problem.

::DEVELOPER

Bio-MIBLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

IEEE Trans Biomed Eng. 2012 Aug 8.
omniBiomarker: a Web-Based Application for Knowledge-Driven Biomarker Identification.
Phan J, Young A, Wang M.

BioPlat 1.1 – Human Cancer Biomarker Discovery

BioPlat 1.1

:: DESCRIPTION

BioPlat (Biomarkers Platform), a user-friendly open-source bioinformatic resource, which provides a set of analytic tools for the discovery and in silico evaluation of novel prognostic and predictive cancer biomarkers based on integration and re-use of gene expression signature in the context of follow-up data.

::DEVELOPER

Cancer Bioinformatics Group

:: SCREENSHOTS

BioPlat

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 BioPlat

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jun 15;30(12):1782-4. doi: 10.1093/bioinformatics/btu111. Epub 2014 Feb 25.
BioPlat: a software for human cancer biomarker discovery.
Butti MD, Chanfreau H, Martinez D, García D, Lacunza E, Abba MC.

BoNB 1.2 – Biomarker Selection and Classification from Genome-wide SNP data

BoNB 1.2

:: DESCRIPTION

BoNB (Bag of Naïve Bayes), an algorithm for genetic biomarker selection and subjects classification from the simultaneous analysis of genome-wide SNP data. BoNB is based on the Naïve Bayes classification framework, enriched by three main features: bootstrap aggregating of an ensemble of Naïve Bayes classifiers, a novel strategy for ranking and selecting the attributes used by each classifier in the ensemble and a permutation-based procedure for selecting significant biomarkers, based on their marginal utility in the classification process. BoNB is tested on the Wellcome Trust Case-Control study on Type 1 Diabetes and its performance is compared with the ones of both a standard Naïve Bayes algorithm and HyperLASSO, a penalized logistic regression algorithm from the state-of-the-art in simultaneous genome-wide data analysis.

::DEVELOPER

Francesco Sambo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 BoNB

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012;13 Suppl 14:S2. doi: 10.1186/1471-2105-13-S14-S2. Epub 2012 Sep 7.
Bag of Naïve Bayes: biomarker selection and classification from genome-wide SNP data.
Sambo F, Trifoglio E, Di Camillo B, Toffolo GM, Cobelli C.

YunBe 1.0 – Gene Set analysis algorithm for Biomarker Identification in the Cloud

YunBe 1.0

:: DESCRIPTION

YunBe is a gene set analysis algorithm for biomarker identification in the cloud (Amazon Web Services).

::DEVELOPER

Laboratory of Cardiovascular research, Luxembourg.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Amazon Web Services

:: DOWNLOAD

 YunBe

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jan 15;28(2):294-5. doi: 10.1093/bioinformatics/btr630. Epub 2011 Nov 13.
Gene set analysis in the cloud.
Zhang L, Gu S, Liu Y, Wang B, Azuaje F.