Tag: Affymetrix

IdeogramBrowser 0.20.4 – Visualization of Genomic Aberrations using Affymetrix SNP Arrays

IdeogramBrowser 0.20.4

:: DESCRIPTION

IdeogramBrowser  was specifically designed for use with the Affymetrix SNP arrays. It provides an interactive karyotypic visualization of multiple aberration profiles and direct links to GeneCards.

::DEVELOPER

Medical Systems Biology, University of Ulm

:: SCREENSHOTS

IdeogramBrowser

:: REQUIREMENTS

  • Windows/MacOsX/Linux
  • Java
:: DOWNLOAD

 IdeogramBrowser

:: MORE INFORMATION

Citation

André Müller, Karlheinz Holzmann and Hans A. Kestler
Visualization of genomic aberrations using Affymetrix SNP arrays
Bioinformatics (2007) 23 (4): 496-497.

Mask / maskBAD 1.36.0 – Mask bad Probes in Affymetrix Expression data

Mask / maskBAD 1.36.0

:: DESCRIPTION

Mask is an R package and contains several functions to handle Affymetrix expression data. Its goal is to mask BAD probes that bias the expression results.

::DEVELOPER

Michael Dannemann, Michael Lachmann @Department of Genetics/Bioinformatics – Max Planck Institut

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Mask

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Apr 16;13:56. doi: 10.1186/1471-2105-13-56.
‘maskBAD’–a package to detect and remove Affymetrix probes with binding affinity differences.
Dannemann M, Lachmann M, Lorenc A.

affylmGUI 1.66.0 – Affymetrix linear modeling Graphical User Interface

affylmGUI 1.66.0

:: DESCRIPTION

affylmGUI is a Graphical User Interface for analysis of Affymetrix microarray data, using the limma package (Linear Models for MicroArray data). affylmGUI is for Affymetrix data only.

::DEVELOPER

WEHI Bioinformatics

:: SCREENSHOTS

affylmGUI

:: REQUIREMENTS

:: DOWNLOAD

 affylmGUI

:: MORE INFORMATION

Citation

affylmGUI: a graphical user interface for linear modeling of single channel microarray data.
Wettenhall JM, Simpson KM, Satterley K, Smyth GK.
Bioinformatics. 2006 Apr 1;22(7):897-9. Epub 2006 Feb 2.

HGNChelper 0.8.1 – Handy functions for working with HGNC Gene Symbols and Affymetrix probeset identifiers

HGNChelper 0.8.1

:: DESCRIPTION

HGNChelper contains functions for identifying and correcting HGNC gene symbols which have been converted to date format by Excel, for reversibly converting between HGNC symbols and valid R names, identifying invalid HGNC symbols and correcting synonyms and outdated symbols which can be mapped to an official symbol.

::DEVELOPER

Waldron lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R package

:: DOWNLOAD

 HGNChelper

:: MORE INFORMATION

Citation

Oh S, Abdelnabi J, Al-Dulaimi R, Aggarwal A, Ramos M, Davis S, Riester M, Waldron L.
HGNChelper: identification and correction of invalid gene symbols for human and mouse.
F1000Res. 2020 Dec 21;9:1493. doi: 10.12688/f1000research.28033.1. PMID: 33564398; PMCID: PMC7856679.

rCGH 1.22.0 – Analyzing and Visualizing Agilent and Affymetrix Array-Based CGH Data

rCGH 1.22.0

:: DESCRIPTION

rCGH is a comprehensive array-based comparative genomic hybridization analysis workflow, integrating computational improvements and functionalities specifically designed for precision medicine.

aCGH_viewer – visualize aCGH profiles from uploaded segmentation tables.

::DEVELOPER

Frederic Commo <frederic.commo at gustaveroussy.fr>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Mac OsX / Linux
  • R/ BioConductor

:: DOWNLOAD

 rCGH, aCGH_viewer

:: MORE INFORMATION

Citation

rCGH: a comprehensive array-based genomic profile platform for precision medicine.
Commo F, Guinney J, Ferté C, Bot B, Lefebvre C, Soria JC, André F.
Bioinformatics. 2015 Dec 26. pii: btv718.

Starr 1.38.0 – Simple Tiling ARRay analysis of Affymetrix ChIP-chip data

Starr 1.38.0

:: DESCRIPTION

Starr is open-source R/Bioconductor package that facilitates comparative analysis of ChIP-chip data across experiments and across different microarray platforms.

::DEVELOPER

Starr  team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 Starr

:: MORE INFORMATION

Citation

Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data.
Zacher B, Kuan PF, Tresch A.
BMC Bioinformatics. 2010 Apr 17;11:194. doi: 10.1186/1471-2105-11-194.

SNPannotator 20090828 – Adding Physical and Genetic Position data to Affymetrix Genotype files

SNPannotator 20090828

:: DESCRIPTION

SNPannotator is designed to annotate the text output files from Affymetrix SNP 6.0 chips. These files are no longer annotated by the Affymetrix console, and so cannot be used by the other programs listed here.

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

SNPannotator

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0

:: DOWNLOAD

 SNPannotator

:: MORE INFORMATION

Illumina2Affy v1/v2/v3 – Converts Illumina files into Affymetrix-style file.

Illumina2Affy v1/v2/v3

:: DESCRIPTION

Illumina2Affy converts Illumina files containing ONE/MULTIPLE individual’s genotype data of the format shown below into an Affymetrix-style file.

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

Illumina2Affy

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0

:: DOWNLOAD

   Illumina2Affy

:: MORE INFORMATION

crlmm 1.48.0 – Genotype Calling and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays

crlmm 1.48.0

:: DESCRIPTION

The R package crlmm implements a multilevel model that adjusts for batch effects and provides allele-specific estimates of copy number.

::DEVELOPER

Division of Biostatistics and Bioinformatics – Johns Hopkins University Oncology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 crlmm

:: MORE INFORMATION

Citation

J Stat Softw. 2011 May 1;40(12):1-32.
Using the R Package crlmm for Genotyping and Copy Number Estimation.
Scharpf RB1, Irizarry RA, Ritchie ME, Carvalho B, Ruczinski I.

MMBGX 0.99.26 – Multi-Mapping Bayesian Gene eXpression for Affymetrix whole-transcript arrays

MMBGX 0.99.26

:: DESCRIPTION

MMBGX is a method for estimating expression at the isoform level and detecting differential splicing using whole-transcript Affymetrix arrays.

::DEVELOPER

Dr Ernest Turro

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MMBGX

:: MORE INFORMATION

Citation

MMBGX: a method for estimating expression at the isoform level and detecting differential splicing using whole-transcript Affymetrix arrays.
Turro E, Lewin A, Rose A, Dallman MJ, Richardson S.
Nucleic Acids Res. 2010 Jan;38(1):e4.