PreProcessing
From Bioalgorithm.com
| Package | Maintainer | Title |
|---|---|---|
| ABarray | Yongming Andrew Sun | Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Micorarray (AB1700) gene expression data. |
| affy | Rafael A. Irizarry | Methods for Affymetrix Oligonucleotide Arrays |
| affycomp | Rafael A. Irizarry | Graphics Toolbox for Assessment of Affymetrix Expression Measures |
| affycoretools | James W. MacDonald | Functions useful for those doing repetitive analyses with Affymetrix GeneChips. |
| affylmGUI | Keith Satterley | GUI for affy analysis using limma package |
| affypdnn | Laurent | Probe Dependent Nearest Neighbours (PDNN) for the affy package |
| affyPLM | Ben Bolstad | Methods for fitting probe-level models |
| altcdfenvs | Laurent Gautier | alternative cdfenvs |
| applera | Francesca Cordero | applera |
| aroma.light | Henrik Bengtsson | Light-weight methods for normalization and visualization of microarray data using only basic R data types |
| arrayMagic | Andreas Buness | two-colour cDNA array quality control and preprocessing |
| beadarray | Mark Dunning | Quality control and low-level analysis of BeadArrays |
| beadarraySNP | Jan Oosting | Normalization and reporting of Illumina SNP bead arrays |
| BeadExplorer | Gareth Elvidge | QC, normalisation, annotation and exploration of Illumina BeadChip data |
| cellHTS | Ligia Bras | Analysis of cell-based screens |
| codelink | Diego Diez | Manipulation of Codelink Bioarrays data. |
| gcrma | Z. Wu | Background Adjustment Using Sequence Information |
| genArise | IFC Development Team | Microarray Analysis tool |
| Harshlight | Maurizio Pellegrino | A "corrective make-up" program for microarray chips |
| limma | Gordon Smyth | Linear Models for Microarray Data |
| limmaGUI | Keith Satterley | GUI for limma package |
| LMGene | Geun Cheol Lee | LMGene Software for Date Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays |
| maCorrPlot | Alexander Ploner | Visualize artificial correlation in microarray data |
| makecdfenv | James W. MacDonald | CDF Environment Maker |
| MANOR | Pierre Neuvial | CGH Micro-Array NORmalization |
| marray | Yee Hwa (Jean) Yang | Exploratory analysis for two-color spotted microarray data |
| mmgmos | Xuejun Liu | multi-chip modified gamma Model of Oligonucleotide Signal |
| nnNorm | Tarca Laurentiu | Spatial and intensity based normalization of cDNA microarray data based on robust neural nets |
| OLIN | Matthias Futschik | Optimized local intensity-dependent normalisation of two-color microarrays |
| OLINgui | Matthias Futschik | Graphical user interface for OLIN |
| rama | Raphael Gottardo | Robust Analysis of MicroArrays |
| SAGx | Per Broberg | Statistical Analysis of the GeneChip |
| simpleaffy | Crispin Miller | Very simple high level analysis of Affymetrix data |
| snapCGH | Mike Smith | Segmentation, normalisation and processing of aCGH data. |
| spotSegmentation | Chris Fraley | Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots |
| stepNorm | Yuanyuan Xiao | Stepwise normalization functions for cDNA microarrays |
| tilingArray | W. Huber | Analysis of high-density oligonucleotide tiling arrays |
| vsn | Wolfgang Huber | Variance stabilization and calibration for microarray data |
Data preprocessing software (in alphabetical order)
- Data munging tools - A number of data munging tools for microarray data. All have perl/tk graphical user interfaces, written by Charlie Kim at Falkow Lab, Stanford University.
- Excel - can handle/ generate larger tab-delimited text files, very useful tool for manipulating raw data.
- Gene Expression Pattern Preprocessor - a web-based tool and it performs scale transformation, replicate handling, missing value imputation, flat pattern filtering and pattern normalisation, written by Bioinformatics Unit of CNIO. There is alsoa Pre-analyse module which performs several checks and plots several histograms to help and to guide the user through the options. The final result can be automatically sent to their local analysis tools and to the EBI EPCLUST. Reference [PubMed]
- Mergem - a perl utility for merging big data files by UC Irvine; you can also use their web interface to do so if you hate UNIX
- Microhelper 1.02 - a tool for merging, filter, normalize, transform, handle missing, select subset, remove control and annotate data, written by Chang Bioscience
- MIDAS (Microarray Data Analysis System) - TIGR Microarray Data Analysis System (MIDAS) is a microarray data quality filtering and normalization tool that allows raw experimental data to be processed through various data normalizations, filters, and transformations via a user-designed analysis pipeline. MIDAS is implemented by Java language. It requires JDK v1.3.1 or higher. MIDAS is written by The Institute of Genomic Research (TIGR). Reference [PubMed]
