vsn 3.61.0 – Normalization and Variance Stabilizing Transformation of Microarray data

vsn 3.61.0

:: DESCRIPTION

vsn (Variance-stabilizing normalization) implements a method for normalising microarray intensities, both between colours within array, and between arrays.

::DEVELOPER

Huber Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ WIndows/MacOsX
R package
BioConductor

:: DOWNLOAD

vsn

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2008 Feb;36(2):e11. doi: 10.1093/nar/gkm1075. Epub 2008 Jan 4.
Model-based variance-stabilizing transformation for Illumina microarray data.
Lin SM, Du P, Huber W, Kibbe WA.

SUMO 1.60i – A Statistical Utility for Microarray and Omics data

SUMO 1.60i

:: DESCRIPTION

SUMO (Statistical Utility for Micro array and Omics data) finds genes / conditions which show statistical differences in their expression between different groups of conditions / genes.

::DEVELOPER

Christian Schwager, Ph. D.

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

SUMO

:: MORE INFORMATION

Citation

Radiat Oncol. 2012 May 17;7:70. doi: 10.1186/1748-717X-7-70.
Identification of stable endogenous control genes for transcriptional profiling of photon, proton and carbon-ion irradiated cells.
Sharungbam GD, Schwager C, Chiblak S, Brons S, Hlatky L, Haberer T, Debus J, Abdollahi A.

ChipSkipper 2.0 – Microarray Image analysis

ChipSkipper 2.0

:: DESCRIPTION

ChipSkipper combines all tasks required for analysis and quantitation of micro-array data – both DNA or protein arrays. It’s image processing routines may be also applied to automated evaluation and quantiation of microscopic images.

::DEVELOPER

Christian Schwager, Ph. D.

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

ChipSkipper

:: MORE INFORMATION

MetaOmics – a suite of packages for Microarray and Genomic Meta-analysis

MetaOmics

:: DESCRIPTION

MetaOmics is a suite of three R packages MetaQC, MetaDE and MetaPath, for quality control, differentially expressed gene identification and enriched pathway detection for microarray meta-analysis.

::DEVELOPER

George C. Tseng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsx
R Package /Java

:: DOWNLOAD

MetaOmics

:: MORE INFORMATION

Citation

Xingbin Wang, Dongwan Kang, Kui Shen, Chi Song, Shuya Lu, Lunching Chang, Serena G. Liao, Zhiguang Huo, Naftali Kaminski, Etienne Sibille, Yan Lin, Jia Li* and George C. Tseng*. (2012)
A Suite of R Packages for Quality Control, Differentially Expressed Gene and Enriched Pathway Detection in Microarray Meta-analysis.
Bioinformatics. 28:2534-2536.

SPD V2 – Sample Progression Discovery underlying Microarray Gene Expression data

SPD V2

:: DESCRIPTION

SPD (Sample Progression Discovery) is a software to discover patterns of biological progression underlying microarray gene expression data

::DEVELOPER

Peng Qiu

:: SCREENSHOTS

:: REQUIREMENTS

Windows
Matlab

:: DOWNLOAD

SPD

:: MORE INFORMATION

Citation

Peng Qiu, Anderw Gentles and Sylvia Plevritis,
“Discovering Biological Progression underlying Microarray Samples“,
PLoS Computational Biology, vol. 7, issue 4, e1001123, 2011.

maSigPro 1.62.0 – R package for the analysis of Microarray and RNA-seq Time Series data

maSigPro 1.62.0

:: 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.

MASQOT-GUI 1.0.1 – Two-channel Microarray Spot Quality Control

MASQOT-GUI 1.0.1

:: DESCRIPTION

MASQOT-GUI provides an open-source, platform-independent software pipeline for two-channel microarray spot quality control. This includes gridding, segmentation, quantification, quality assessment and data visualization. It hosts three independent applications (MASQOTGrid, MASQOTSeg and MASQOTView) for this purpose with interactions between the tools as well as import and export support for external software.

::DEVELOPER

MASQOT-GUI team

:: SCREENSHOTS

:: REQUIREMENTS

Windows/Linux/MacOsX
Java

:: DOWNLOAD

MASQOT-GUI

:: MORE INFORMATION

Citation

Bioinformatics. 2006 Oct 15;22(20):2554-5. Epub 2006 Aug 9.
MASQOT-GUI: spot quality assessment for the two-channel microarray platform.
Bylesjö M1, Sjödin A, Eriksson D, Antti H, Moritz T, Jansson S, Trygg J.

BNArray 1.0 – Constructing Gene Regulatory Networks from Microarray data by using Bayesian network

BNArray 1.0

:: DESCRIPTION

BNArray is a systemized tool developed in R. It facilitates the construction of gene regulatory networks from DNA microarray data by using Bayesian network. Significant submodules of regulatory networks with high confidence are reconstructed using our extended sub-network mining algorithm for directed graphs.

::DEVELOPER

Ming Chen’s Bioinformatics Group, Zhejiang University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux/MacOsX
R package

:: DOWNLOAD

BNArray

:: MORE INFORMATION

Citation

Bioinformatics. 2006 Dec 1;22(23):2952-4.
BNArray: an R package for constructing gene regulatory networks from microarray data by using Bayesian network.
Chen X, Chen M, Ning K.

GEOmetadb 1.52.0 – GEO Microarray Search Tool

GEOmetadb 1.52.0

:: DESCRIPTION

GEOmetadb is an attempt to make access to the metadata associated with the NCBI Gene Expression Omnibus (GEO) samples, platforms, and datasets much more feasible for common biologists and bioinformatians/statistians.

::DEVELOPER

Jack Zhu , Sean Davis @NCI

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux/ Windows/ MacOsX
R package
BioConductor

:: DOWNLOAD

GEOmetadb

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Dec 1;24(23):2798-800. doi: 10.1093/bioinformatics/btn520.
GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus.
Zhu Y, Davis S, Stephens R, Meltzer PS, Chen Y.

Re-Annotator 1.0.0 – Re-annotates Microarray Probes

Re-Annotator 1.0.0

:: DESCRIPTION

Re-Annotator is a re-annotation pipeline for gene expression microarrays that will bring probe annotations up-to-date!

::DEVELOPER

André Altmann

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Linux
Perl, BWA,SAMtools,Annovar

:: DOWNLOAD

Re-Annotator

:: MORE INFORMATION

Citation

Re-Annotator: Annotation Pipeline for Microarray Probe Sequences.
Arloth J, Bader DM, Röh S, Altmann A.
PLoS One. 2015 Oct 1;10(10):e0139516. doi: 10.1371/journal.pone.0139516