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.

DNorm 0.0.7 – Disease Name Normalization

DNorm 0.0.7

:: DESCRIPTION

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

::DEVELOPER

Zhiyong Lu

:: 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.

snm 1.38.0 – Supervised Normalization of Microarrays

snm 1.38.0

:: 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.

NVT 1.0 – R package for the Assessment of RNA-Seq Normalization methods

NVT 1.0

:: DESCRIPTION

NVT (NORMALIZATION VISUALIZATION TOOL) is an R package for the assessment of RNA-Seq normalization methods.

::DEVELOPER

CUBE – Bioinformatics and Computational Systems Biology, University of Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R

:: DOWNLOAD

NVT

:: MORE INFORMATION

Citation:

Bioinformatics, 32 (23), 3682-3684 2016 Dec 1
NVT: A Fast and Simple Tool for the Assessment of RNA-seq Normalization Strategies
Thomas Eder, Florian Grebien, Thomas Rattei

SPANS 1.0 – Statistical Procedure for the Analyses of peptide abundance Normalization Strategies

SPANS 1.0

:: DESCRIPTION

SPANS is an approach to evaluate normalization strategies, which includes the peptide selection component associated with the derivation of normalization values. The approach evaluates the effect of normalization on the between-group variance structure in order to identify the most appropriate normalization methods that improve the structure of the data without introducing bias into the normalized peak intensities.

::DEVELOPER

Computational Biology & Bioinformatics ,Pacific Northwest National Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Java
  • matlab

:: DOWNLOAD

 SPANS

:: MORE INFORMATION

SNOMAD – Standardization & Normalization of Microarray Data

SNOMAD

:: DESCRIPTION

SNOMAD is a program for the standardization and normalization of gene expression datasets. In addition to conventional transformations and visualization tools, SNOMAD includes two non-linear transformations which correct for bias and variance which are non-uniformly distributed across the range of microarray element signal intensities: local mean normalization and local variance correction (Z-score generation using a locally calculated standard deviation).

::DEVELOPER

the Pevsner Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R package

:: DOWNLOAD

 SNOMAD

:: MORE INFORMATION

Citation

Bioinformatics. 2002 Nov;18(11):1540-1.
SNOMAD (Standardization and NOrmalization of MicroArray Data): web-accessible gene expression data analysis.
Colantuoni C, Henry G, Zeger S, Pevsner J.

LINNAEUS 2.0 – Species Name Recognition and Normalization software

LINNAEUS 2.0

:: DESCRIPTION

LINNAEUS is a general-purpose dictionary matching software, capable of processing multiple types of document formats in the biomedical domain (MEDLINE, PMC, BMC, OTMI, text, etc.). It can produce multiple types of output (XML, HTML, tab-separated-value file, or save to a database). It also contains methods for acting as a server (including load balancing across several servers), allowing clients to request matching over a network. A package with files for recognizing and identifying species names is available for LINNAEUS, showing 94% recall and 97% precision compared to LINNAEUS-species-corpus.

::DEVELOPER

the Bergman lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 LINNAEUS

:: MORE INFORMATION

Citation

Martin Gerner, Goran Nenadic and Casey M Bergman
LINNAEUS: A species name identification system for biomedical literature
BMC Bioinformatics 2010, 11:85

GNAT 1.22 – Gene / Protein Named Entity Recognition and Normalization software

GNAT 1.22

:: DESCRIPTION

GNAT (Gene Name Normalization) is a library and web service capable of performing gene entity NER and normalization of biomedical articles. Mentions of genes and proteins in the articles are linked to to Entrez Gene identifiers.

::DEVELOPER

the Bergman lab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 GNAT

:: MORE INFORMATION

Citation

Hakenberg et al. (2011)
The GNAT library for local and remote gene mention normalization
Bioinformatics (2011) 27 (19): 2769-2771.

XPN – Merging Two Gene-expression studies via cross-platform normalization

XPN

:: DESCRIPTION

XPN is a cross-platform normalization method for combining gene expression data from different studies. Merging two gene-expression studies via cross-platform normalization.

:DEVELOPER

Andrey A. Shabalin

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

 XPN

:: MORE INFORMATION

Citation

A.A. Shabalin, H. Tjelmeland, C. Fan, C.M. Perou, and A.B. Nobel.
Merging two gene-expression studies via cross-platform normalization.
Bioinformatics, 24(9):1154, 2008

noRNAlize 1.0 – RNA SHAPE Data Normalization software

noRNAlize 1.0

:: DESCRIPTION

noRNAlize is a data analysis package to analyze and normalize SHAPE (Selective 2′-Hydroxyl Acylation and Primer Extension) data. Traditionally, SHAPE requires the addition of a 3′ hairpin to the RNA for normalization. noRNAlize elminates the need for this experimental step by performing a global analysis of the SHAPE data, and establishing mean protection values. This is particularly important when SHAPE analysis is used to map crystal contacts in crystal structures as illustrated here.

::DEVELOPER

noRNAlize Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX /  Linux
  • MATLAB

:: DOWNLOAD

 noRNAlize

:: MORE INFORMATION

Citation:

Vicens Q, Gooding AR, Laederach A, Cech TR,
Local RNA structural changes induced by crystallization are revealed by SHAPE,
RNA, (2007)