Tag: Normalisation

SMETHILLIUM 1.2 – Spatial normalisation METHod for ILLumina InfinIUM HumanMethylation BeadChip

SMETHILLIUM 1.2

:: DESCRIPTION

SMETHILLIUM is a  spatial normalisation method for ILLumina InfinIUM HumanMethylation BeadChip. DNA methylation is a major epigenetic modification in human cells. Illumina HumanMethylation27 BeadChip investigates the methylation of 27,578 loci in the genome. We developed a normalisation method to correct the spatial background noise which affect the signal-to-noise ratio. The prediction performance of the proposed method was assessed on methylated and unmethylated samples. We demonstrate that the spatial normalisation outperforms BeadStudio to predict the methylation status of a given locus

::DEVELOPER

Computational Systems Biology of Cancer group in Bioinformatics Laboratory of Institut Curie (Paris).

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  SMETHILLIUM

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Jun 15;27(12):1693-5. Epub 2011 Apr 14.
SMETHILLIUM: spatial normalization method for Illumina infinium HumanMethylation BeadChip.
Sabbah C, Mazo G, Paccard C, Reyal F, Hupé P.

snapCGH 1.62.0- Segmentation, Normalisation And Processing of Array CGH data

snapCGH 1.62.0

:: DESCRIPTION

snapCGH is a softwaer for the analysis of array CGH data. It has been written to be compatible with limma so that the user can apply all of the preprocessing functions available within limma to array CGH data.

::DEVELOPER

snapCGH team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 snapCGH

:: MORE INFORMATION

ReadqPCR / NormqPCR 1.38.0 / – Read qPCR data / Functions for Normalisation of RT-qPCR data

ReadqPCR / NormqPCR 1.38.0

:: DESCRIPTION

ReadqPCR and NormqPCR are R/Bioconductor packages to analyse RT-qPCR data.

::DEVELOPER

James Perkins <j.perkins at ucl.ac.uk>, Matthias Kohl, Nor Izayu Abdul Rahman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 ReadqPCR and NormqPCR

:: MORE INFORMATION

Citation

BMC Genomics. 2012 Jul 2;13:296. doi: 10.1186/1471-2164-13-296.
ReadqPCR and NormqPCR: R packages for the reading, quality checking and normalisation of RT-qPCR quantification cycle (Cq) data.
Perkins JR1, Dawes JM, McMahon SB, Bennett DL, Orengo C, Kohl M.

Realyser 1.0 – Real Time PCR Normalisation tool

Realyser 1.0

:: DESCRIPTION

Realyser is a program to help with the selection of stable controls for QPCR and the normalisation of QPCR data. It is an application of the GNorm technique and is designed to work with the data files from ABI Real-time PCR machines.

:: DEVELOPER

Babraham Bioinformatics

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Mac OsX/Windows
  • Java 

:: DOWNLOAD

 Realyser

:: MORE INFORMATION

Arrayplot 3.01 – Visalisuation and Normalisation of Microarray data

Arrayplot 3.01

:: DESCRIPTION

Arrayplot has been designed to allow rapid visalisuation and normalisation of microarray data. It provides a user-friendly interface to visualise data distribution and to view most variant genes. It permits to calculate normalisation factor based on overall median intensity.

::DEVELOPER

Jacq’s group

:: SCREENSHOTS

Arrayplot

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Arrayplot

:: MORE INFORMATION

Citation

Bioinformatics. 2002 Jun;18(6):888-9.
Arrayplot for visualization and normalization of cDNA microarray data.
Marc P, Jacq C.

Istvan – Normalisation of Expression Data

Istvan

:: DESCRIPTION

Istvan is a collection of modules implementing various methods for inferring an invariant set, i.e. a set of genes with no or little difference in actual expression levels, from a set of pairs of microarray measured expression levels, and for inferring normalising functions based on a set of pairwise data, possibly an invariant set determined by one of the implemented methods.

::DEVELOPER

Rune Lyngsø

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX\
  • C Compiler

:: DOWNLOAD

 Istvan

:: MORE INFORMATION

ArrayNorm 1.7.6 – Normalisation and Statistical Analysis for Microarray-experiment data

ArrayNorm 1.7.6

:: DESCRIPTION

ArrayNorm is an platform-independent Java tool for normalisation and statistical analysis for microarray-experiment data. It provides modules for visualization (scatterplot, histogram, boxplot, etc.), normalization and analysis. The user can upload any number of microarray-datasets, resulting from one experiment. According to experimental design and relationships between the microarrays, the data is organized for later analysis and replicate handling. Arraynorm features a variety of normalization methods, such as ‘global median’, ‘dyeswap-pairs normalization’, ‘lowess fitting’ and ‘normalization using control-spots’. Differentially expressed genes can be found using foldchange-detection or statistical tests (t-test). All DE genes can be printed to a textfile, allowing further analysis with other software-tools (like Genesis).

::DEVELOPER

Genomics & Bioinformatics Graz, Graz University of Technology

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / WIndows /MacOsX
  • Java

:: DOWNLOAD

 ArrayNorm

:: MORE INFORMATION

Citation

Pieler R, Sanchez-Cabo F, Hackl H, Thallinger GG, Trajanoski Z.
ArrayNorm: Comprehensive Normalization and Analysis of Microarray Data.
Bioinformatics. 2004. 20:1971-1973.