maSigPro 1.54.0 – R package for the analysis of Microarray and RNA-seq Time Series data

maSigPro 1.54.0

:: DESCRIPTION

maSigPro (MicroArray Significant Profiles)is a regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray experiments.

::DEVELOPER

The Genomics of Gene Expression Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R Package
  • BioConductor

:: DOWNLOAD

 maSigPro

:: MORE INFORMATION

Citation

Next maSigPro: updating maSigPro Bioconductor package for RNA-seq time series.
Nueda MJ, Tarazona S, Conesa A.
Bioinformatics. 2014 Jun 3. pii: btu333.

Bioinformatics. 2006 May 1;22(9):1096-102. Epub 2006 Feb 15.
maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments.
Conesa A1, Nueda MJ, Ferrer A, Talón M.

PUMA 3.14.0 – Propagating Uncertainty in Microarray Analysis

PUMA 3.14.0

:: DESCRIPTION

puma is a Bioconductor package incorporating a suite of analysis methods for use on Affymetrix GeneChip data.

:: DEVELOPER

BIOINFORMATICS @ MANCHESTER

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / windows/ MacOsX
  • BioConductor
  • R package

:: DOWNLOAD

 PUMA

:: MORE INFORMATION

Citation

puma: a Bioconductor package for propagating uncertainty in microarray analysis.
Pearson RD, Liu X, Sanguinetti G, Milo M, Lawrence ND, Rattray M.
BMC Bioinformatics. 2009 Jul 9;10:211. doi: 10.1186/1471-2105-10-211.

puma 3.0: improved uncertainty propagation methods for gene and transcript expression analysis.
Liu X, Gao Z, Zhang L, Rattray M.
BMC Bioinformatics. 2013 Feb 5;14:39. doi: 10.1186/1471-2105-14-39

hapLOH 1.3 – Analysis of loss of Heterozygosity in Tumor Genomes

hapLOH 1.3

:: DESCRIPTION

hapLOH profiles and characterizes tumor genomes using data from SNP microarrays. It is designed to be effective in the presence of high levels of germline contamination.

::DEVELOPER

paul scheet lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Perl
  • Python

:: DOWNLOAD

  hapLOH

:: MORE INFORMATION

Citation

Vattathil, Selina, and Paul Scheet.
Haplotype-based profiling of subtle allelic imbalance with SNP arrays.
Genome research 23.1 (2013): 152-158.

QuSAGE 2.4.0 – Quantitative Set Analysis for Gene Expression

QuSAGE 2.4.0

:: DESCRIPTION

QuSAGE is a novel Gene Set Enrichment-type test, which is designed to provide a faster, more accurate, and easier to understand test for gene expression studies.

::DEVELOPER

Kleinstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 QuSAGE

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Oct;41(18):e170. doi: 10.1093/nar/gkt660. Epub 2013 Aug 5.
Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations.
Yaari G1, Bolen CR, Thakar J, Kleinstein SH.

HAMSTER 1.3.0 – Helpful Abstraction using Minimum Spanning Trees for Expression Relations

HAMSTER 1.3.0

:: DESCRIPTION

HAMSTER is a tool for depicting experiments in a microarray data set as a set of minimum spanning trees.

::DEVELOPER

Raymond Wan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • C++ Compiler

:: DOWNLOAD

HAMSTER

:: MORE INFORMATION

Citation

HAMSTER: visualizing microarray experiments as a set of minimum spanning trees.
Wan R, Kiseleva L, Harada H, Mamitsuka H, Horton P.
Source Code Biol Med. 2009 Nov 20;4:8. doi: 10.1186/1751-0473-4-8.

W-ChIPeaks – Process ChIP-chip and ChIP-seq data

W-ChIPeaks

:: DESCRIPTION

W-ChIPeaks employs a probe-based or bin-based enrichment threshold to define peaks and applies statistical methods to control the false discovery rate for identified peaks.

::DEVELOPER

Jin Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Feb 1;27(3):428-30. doi: 10.1093/bioinformatics/btq669. Epub 2010 Dec 7.
W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data.
Lan X, Bonneville R, Apostolos J, Wu W, Jin VX.

FISH Oracle 2 – Visualize Data from multiple Array CGH or SNP Array Experiments

FISH Oracle 2

:: DESCRIPTION

FISH Oracle is a web-based software to visualize data from multiple array CGH or SNP array experiments in a genomic context. Its fast visualization engine and advanced web and database technology supports highly interactive use. FISH Oracle comes with a convenient data import mechanism, powerful search options for genomic elements (like gene names or karyobands), quick navigation and  zooming into interesting regions, and mechanisms to export the visualization into different high quality image formats (PDF, PS, PNG, SVG).

::DEVELOPER

RESEARCH GROUP FOR GENOME INFORMATICS ,Center for Bioinformatics, University of Hamburg

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX
  • MySQL
  • Java
  • Apache Tomcat server
  • GenomeTools

:: DOWNLOAD

  FISH Oracle

:: MORE INFORMATION

Citation

M. Mader, R. Simon, S. Steinbiss and S. Kurtz:
FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context.
Journal of Clinical Bioinformatics, 1:20 (2011)

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

GeneTrail / GeneTrailExpress – Gene Set Analysis tool / for pre-processing Microarray data

GeneTrail / GeneTrailExpress

:: DESCRIPTION

GeneTrail is a comprehensive and efficient gene set analysis tool that offers a rich functionality and is easy to use.

GeneTrailExpress provides comprehensive normalization and scoring functions for pre-processing microarray data. The processed data is directly passed to GeneTrail for statistical evaluation in an extensive gene set analysis.

::DEVELOPER

Chair for clinical bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2008 Dec 22;9:552. doi: 10.1186/1471-2105-9-552.
GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments.
Keller A1, Backes C, Al-Awadhi M, Gerasch A, Küntzer J, Kohlbacher O, Kaufmann M, Lenhof HP.

Backes C, Keller A, Kuentzer J, Kneissl B, Comtesse N, Elnakady YA, Müller R, Meese E, Lenhof HP.
GeneTrail–advanced gene set enrichment analysis.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W186-92.

rCGH 1.0.2 – Analyzing and Visualizing Agilent and Affymetrix Array-Based CGH Data

rCGH 1.0.2

:: DESCRIPTION

rCGH is a comprehensive array-based comparative genomic hybridization analysis workflow, integrating computational improvements and functionalities specifically designed for precision medicine.

aCGH_viewer – visualize aCGH profiles from uploaded segmentation tables.

::DEVELOPER

Frederic Commo <frederic.commo at gustaveroussy.fr>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Mac OsX / Linux
  • R/ BioConductor

:: DOWNLOAD

 rCGHaCGH_viewer

:: MORE INFORMATION

Citation

rCGH: a comprehensive array-based genomic profile platform for precision medicine.
Commo F, Guinney J, Ferté C, Bot B, Lefebvre C, Soria JC, André F.
Bioinformatics. 2015 Dec 26. pii: btv718.