TCC 1.10.0 – Differential Expression Analysis for Tag Count data with Robust Normalization Strategies

TCC 1.10.0

:: DESCRIPTION

TCC provides a series of functions for performing differential expression analysis from RNA-seq count data using robust normalization strategy (called DEGES).

::DEVELOPER

Jianqiang Sun <wukong at bi.a.u-tokyo.ac.jp>, Tomoaki Nishiyama <tomoakin at staff.kanazawa-u.ac.jp>, Koji Kadota

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 TCC

:: MORE INFORMATION

Citation

TCC: an R package for comparing tag count data with robust normalization strategies.
Sun J, Nishiyama T, Shimizu K, Kadota K.
BMC Bioinformatics. 2013 Jul 9;14:219. doi: 10.1186/1471-2105-14-219.

snm 1.18.0 – Supervised Normalization of Microarrays

snm 1.18.0

:: DESCRIPTION

SNM is a modeling strategy especially designed for normalizing high-throughput genomic data.

::DEVELOPER

STOREY LAB | Princeton University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 SNM

:: MORE INFORMATION

Citation

Bioinformatics. 2010 May 15;26(10):1308-15. doi: 10.1093/bioinformatics/btq118. Epub 2010 Mar 31.
Supervised normalization of microarrays.
Mecham BH1, Nelson PS, Storey JD.

funtooNorm 0.99.1 – Normalization of Illumina Infinium Human Methylation 450 BeadChip

funtooNorm 0.99.1

:: DESCRIPTION

The R package funtooNorm provides a function for normalization of Illumina Infinium Human Methylation 450 BeadChip (Illumina 450K) data when there are samples from multiple tissues or cell types.

::DEVELOPER

Greenwood Lab, Statistical Genetics at the Lady Davis Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/  MacOSX
  • R

:: DOWNLOAD

 funtooNorm

:: MORE INFORMATION

Citation

funtooNorm: an R package for normalization of DNA methylation data when there are multiple cell or tissue types.
Oros Klein K, Grinek S, Bernatsky S, Bouchard L, Ciampi A, Colmegna I, Fortin JP, Gao L, Hivert MF, Hudson M, Kobor MS, Labbe A, MacIsaac JL, Meaney MJ, Morin AM, O’Donnell KJ, Pastinen T, Van Ijzendoorn MH, Voisin G, Greenwood CM.
Bioinformatics. 2015 Oct 24. pii: btv615.

MetTailor 1.0 – Dynamic Block Summary and Data Normalization for Robust Analysis

MetTailor 1.0

:: DESCRIPTION

MetTailor is a software package that performs post-extraction processing steps such as cross-sample realignment and data normalization that are specifically designed to account for the experimental factors from chromatographic separation and MS analysis.

::DEVELOPER

MetTailor team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • R

:: DOWNLOAD

 MetTailor

:: MORE INFORMATION

Citation

MetTailor: Dynamic Block Summary and Intensity Normalization for Robust Analysis of Mass Spectrometry Data in Metabolomics.
Chen G, Cui L, Teo G, Ong CN, Tan CS, Choi H.
Bioinformatics. 2015 Jul 27. pii: btv434.

DNorm 0.0.6 – Disease Name Normalization

DNorm 0.0.6

:: DESCRIPTION

DNorm is an automated method for determining which diseases are mentioned in biomedical text, the task of disease normalization.

::DEVELOPER

Robert Leaman , Rezarta Islamaj Doǧan and Zhiyong Lu, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

 DNorm

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Nov 15;29(22):2909-17. doi: 10.1093/bioinformatics/btt474. Epub 2013 Aug 21.
DNorm: disease name normalization with pairwise learning to rank.
Leaman R, Islamaj Dogan R, Lu Z.

nnNorm 2.32.0 – Spatial and Intensity based Normalization of cDNA Microarray data

nnNorm 2.32.0

:: DESCRIPTION

nnNorm is an algorithm designed to remove intensity and spatial dependent biases from microarray expression data sets. It uses robust neural networks to fit the log-ratios on spatial coordinates and log-average intensity of the cDNA spots.

::DEVELOPER

the Bioinformatics and Computational Biology Unit of the Perinatology Research Branch (NICHD)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • R package
  • Bioconductor

:: DOWNLOAD

  nnNorm

:: MORE INFORMATION

Citation

Tarca AL, Cooke JE, Mackay J.
A robust neural networks approach for spatial and intensity-dependent normalization of cDNA microarray data.
Bioinformatics 2005;21(11):2674-83.

vsn 3.37.0 – Normalization and Variance Stabilizing Transformation of Microarray data

vsn 3.37.0

:: 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.

MANOR 1.40.0 – Micro-Array NORmalization of array-CGH data

MANOR 1.40.0

:: DESCRIPTION

MANOR (Micro-Array NORmalization) is a software which is devoted to the normalization of Array Comparative Genomic Hybridization (array-CGH) data.

::DEVELOPER

U900 Institut Curie – INSERM/Mines ParisTech “Bioinformatics and Computational Systems Biology of Cancer

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R package
  • Bioconductor

:: DOWNLOAD

 MANOR

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2006 May 22;7:264.
Spatial normalization of array-CGH data.
Neuvial P, Hupé P, Brito I, Liva S, Manié E, Brennetot C, Radvanyi F, Aurias A, Barillot E.

TurboNorm 1.16.0 – A fast Scatterplot Smoother Suitable for Microarray Normalization

TurboNorm 1.16.0

:: DESCRIPTION

TurboNorm is a software for fast scatterplot smoother based on B-splines with second-order difference penalty.

::DEVELOPER

Microarray Analysis Group, Center for Human and Clinical Genetics – LUMC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 TurboNorm

:: MORE INFORMATION

Citation

Stat Appl Genet Mol Biol. 2012 Jul 12;11(4). pii: /j/sagmb.2012.11.issue-4/1544-6115.1753/1544-6115.1753.xml. doi: 10.1515/1544-6115.1753.
A novel and fast normalization method for high-density arrays.
van Iterson M, Duijkers FA, Meijerink JP, Admiraal P, van Ommen GJ, Boer JM, van Noesel MM, Menezes RX.

Rsolid 0.9-31 – Normalization and Base Calling for ABI SOLiD data

Rsolid 0.9-31

:: DESCRIPTION

Rsolid is a R package for normalizing fluorescent intensity data from ABI/SOLiD second generation sequencing platform. It has been observed that the color-calls provided by factory software contain technical artifacts, where the proportions of colors called are extremely variable across sequencing cycles.
Rafael Irizarry’s Lab

::DEVELOPER

Hao Wu, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /Linux/ MacOsX
  • R

:: DOWNLOAD

  Rsolid

:: MORE INFORMATION

Citation

Nat Methods. 2010 May;7(5):336-7. doi: 10.1038/nmeth0510-336.
Intensity normalization improves color calling in SOLiD sequencing.
Wu H, Irizarry RA, Bravo HC.