SSPA 2.32.1 – Power and Sample Size analysis for Microarray Experiments on the basis of Pilot data

SSPA 2.32.1

:: DESCRIPTION

SSPA : General Sample size and power analysis for microarray and next-generation sequencing data.

::DEVELOPER

Maarten van Iterson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 SSPA

:: MORE INFORMATION

Citation

BMC Genomics. 2009 Sep 17;10:439. doi: 10.1186/1471-2164-10-439.
Relative power and sample size analysis on gene expression profiling data.
van Iterson M1, ‘t Hoen PA, Pedotti P, Hooiveld GJ, den Dunnen JT, van Ommen GJ, Boer JM, Menezes RX.

MaRe – Searching and large scale Retrieval of public Microarray data

MaRe

:: DESCRIPTION

MaRe (Microarray Retriever) enables batch retrieval of microarray data matching your search criteria from the seas of data in GEO and ArrayExpress microarray repositories. You can search on accession numbers (GSE, GDS, AE_ACCN, PMID), authors, species, dates, platforms or on keywords of unspecified type.

::DEVELOPER

MaRe team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W327-31. doi: 10.1093/nar/gkn213. Epub 2008 May 7.
Microarray retriever: a web-based tool for searching and large scale retrieval of public microarray data.
Ivliev AE1, ‘t Hoen PA, Villerius MP, den Dunnen JT, Brandt BW.

survGenesInterim 1.0 – Simulation of Survival Studies with Microarray Data

survGenesInterim 1.0

:: DESCRIPTION

survGenesInterim is an R package for simulation of survival studies based on simulated gene expression level and patient data. Includes functions to generate such data. Resulting error and power rate can be visualized.

::DEVELOPER

survGenesInterim team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 survGenesInterim

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Apr 29;12:127. doi: 10.1186/1471-2105-12-127.
Sequential interim analyses of survival data in DNA microarray experiments.
Leha A1, Beissbarth T, Jung K.

QUBIC2 / QUBIC-R 1.20.1 – Biclustering Tool for Microarray Data

QUBIC2 / QUBIC-R 1.20.1

:: DESCRIPTION

QUBIC ( QUalitative BIClustering algorithm) provides a biclustering module for microarray data. For a set of genes and a set of conditions, the program outputs a block-like structure which shows uniform pattern within the block, the block would contain only subsets of all given genes under subsets of all given conditions.

QUBIC2 is a novel biclustering algorithm for analyses of gene expression data from bulk and single-cell RNA-Sequencing.

::DEVELOPER

Qin Ma  , Bioinformatic and Mathematical Biosciences Lab, The Ohio State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

QUBIC2 / QUBIC-R

:: MORE INFORMATION

Citation

Zhang Y, Xie J, Yang J, Fennell A, Zhang C, Ma Q.
QUBIC: a bioconductor package for qualitative biclustering analysis of gene co-expression data.
Bioinformatics. 2017 Feb 1;33(3):450-452. doi: 10.1093/bioinformatics/btw635. PMID: 28172469.

Guojun Li, Qin Ma, Haibao Tang, Andrew H. Paterson, Ying Xu,
QUBIC: A Qualitative Biclustering Algorithm for Analyses of Gene Expression Data,
Nucleic Acids Research, 2009, 37(15): e101-

XMAS – eXperiential Microarray Analysis System

XMAS

:: DESCRIPTION

XMAS is an open-source, platform-independent web application for a new type of interactive, “sit-forward” microarray analysis.

::DEVELOPER

Biocomputing and Media Research Lab

:: SCREENSHOTS

XMAS

:: REQUIREMENTS

  • WEb Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013;14 Suppl 14:S10. doi: 10.1186/1471-2105-14-S14-S10. Epub 2013 Oct 9.
Towards human-computer synergetic analysis of large-scale biological data.
Singh R, Yang H, Dalziel B, Asarnow D, Murad W, Foote D, Gormley M, Stillman J, Fisher S.

LSPR – Detect Periodic Expression Profiles in DNA Microarray Time-series data

LSPR

:: DESCRIPTION

LSPR is a Matlab package used to detect periodic expression profiles in DNA microarray time-series data.

::DEVELOPER

LSPR team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • MatLab

:: DOWNLOAD

  LSPR

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Apr 1;27(7):1023-5. doi: 10.1093/bioinformatics/btr041. Epub 2011 Feb 3.
LSPR: an integrated periodicity detection algorithm for unevenly sampled temporal microarray data.
Yang R1, Zhang C, Su Z.

CAFE 1.28.0 – Detection of Gross Chromosomal Abnormalities from Gene Expression Microarray data

CAFE 1.28.0

:: DESCRIPTION

CAFE (Chromosomal Aberration Finder in Expression data) is an R package for the detection of gross chromosomal gains and losses from expression microarrays, with a resolution up to cytoband level.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ windows/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

  CAFE

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 15;30(10):1484-5. doi: 10.1093/bioinformatics/btu028. Epub 2014 Jan 21.
CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data.
Bollen S1, Leddin M, Andrade-Navarro MA, Mah N.

ReportingTools 2.32.1 – Tools for Making Microarray and Sequencing Data Reports in various Formats

ReportingTools 2.32.1

:: DESCRIPTION

The ReportingTools software package enables users to easily display reports of analysis results generated from sources such as microarray and sequencing data. The package allows users to create HTML pages that may be viewed on a web browser such as Safari, or in other formats readable by programs such as Excel.

:: DEVELOPER

ReportingTools team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX/Windows
  • R package
  • BioConductor

:: DOWNLOAD

  ReportingTools

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Oct 18.
ReportingTools: an automated result processing and presentation toolkit for high-throughput genomic analyses.
Huntley MA, Larson JL, Chaivorapol C, Becker G, Lawrence M, Hackney JA, Kaminker JS.

metaArray 1.66.0 – Integration of Microarray Data for Meta-analysis

metaArray 1.66.0

:: DESCRIPTION

metaArray is a general probabilistic framework for combining high-throughput genomic data from several related microarray experiments using mixture models.

::DEVELOPER

metaArray team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/ WIndows
  • R package
  • BioCOnductor

:: DOWNLOAD

  metaArray

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2007 Sep 27;8:364.
A latent variable approach for meta-analysis of gene expression data from multiple microarray experiments.
Choi H1, Shen R, Chinnaiyan AM, Ghosh D.

limmaGUI 1.68.0 – Linear Models for Microarrays Graphical User Interface

limmaGUI 1.68.0

:: DESCRIPTION

limmaGUI is a Graphical User Interface for Gordon Smyth’s limma package (Linear Models for MicroArray data). It uses state-of-the-art statistical techniques to normalize microarray data, perform diagnostic plots and to find differentially expressed genes in complex experimental designs.

::DEVELOPER

WEHI Bioinformatics

:: SCREENSHOTS

limmaGUI

:: REQUIREMENTS

:: DOWNLOAD

 limmaGUI

:: MORE INFORMATION

Citation

Bioinformatics. 2004 Dec 12;20(18):3705-6. Epub 2004 Aug 5.
limmaGUI: a graphical user interface for linear modeling of microarray data.
Wettenhall JM, Smyth GK.