Data preprocessing is performed on raw array expression data to prevent technical artefacts.

affy
Desktop

affy

Contains functions for the storage, management and analysis of oligonucleotide…

Contains functions for the storage, management and analysis of oligonucleotide arrays. affy provides the user with extreme flexibility when carrying out an analysis and make it possible to access and…

sva
Desktop

sva Surrogate Variable Analysis

Contains functions for removing batch effects and other unwanted variation in…

Contains functions for removing batch effects and other unwanted variation in high-throughput experiment. Specifically, the sva package contains functions for the identifying and building surrogate…

lumi
Desktop

lumi

Provides class infrastructure and associated methods to construct an Illumina…

Provides class infrastructure and associated methods to construct an Illumina analysis workflow pipeline starting with raw data through functional analysis. Besides supporting the existing algorithms…

RPA
Desktop

RPA Robust Probabilistic Averaging

Analyzes the reliability of individual probes directly from gene expression…

Analyzes the reliability of individual probes directly from gene expression data. A major advantage of the proposed approach is its capability to detect unreliable probes independently of physical…

ArrayAnalysis.o…
Desktop
Web

ArrayAnalysis.org

Provides researchers with an easy-to-use and comprehensive interface to the…

Provides researchers with an easy-to-use and comprehensive interface to the functionality of R and Bioconductor packages for microarray data analysis. As a modular open source project, it allows…

arrayQualityMet…
Desktop

arrayQualityMetrics

A package that provides a report with diagnostic plots for one or two colour…

A package that provides a report with diagnostic plots for one or two colour microarray data. After preparation of the data, a single command line is used to create the report. The quality metrics…

dyebias
Desktop

dyebias

A correction method whereby sequence-specific corrections are modulated by the…

A correction method whereby sequence-specific corrections are modulated by the overall bias of individual hybridizations. GASSCO outperforms earlier methods and works well on a variety of publically…

CoGAPS
Desktop

CoGAPS Coordinated Gene Activity in Pattern Sets

An R/C++ package to identify patterns and biological process activity in…

An R/C++ package to identify patterns and biological process activity in transcriptomic data. CoGAPS provides an integrated package for isolating gene expression driven by a biological process,…

ISVA
Desktop

ISVA Independent Surrogate Variable Analysis

Identifies features correlating with a phenotype of interest in the presence of…

Identifies features correlating with a phenotype of interest in the presence of potential confounding factors. Using simulated data, we show that ISVA performs well in identifying confounders as well…

snm
Desktop

snm Supervised Normalization of Microarrays

Provides a modeling strategy especially designed for normalizing…

Provides a modeling strategy especially designed for normalizing high-throughput genomic data. The underlying premise of our approach is that the data is a function of what they refer to as…

G T A T C G C T A
quantro
Desktop

quantro

Provides a data-driven solution to test the assumptions of global normalization…

Provides a data-driven solution to test the assumptions of global normalization methods. Group level information about each sample (such as tumor/normal status) must be provided because the test…

OLINgui
Desktop

OLINgui

Graphical user interface for the OLIN package.

Graphical user interface for the OLIN package.

OLIN
Desktop
arrayMagic
Desktop

arrayMagic

Facilitates the analysis of two colour cDNA microarray data. It aims to provide…

Facilitates the analysis of two colour cDNA microarray data. It aims to provide quality assured and normalized data. arrayMagic bridges the gap between the image quantification software and…

bapred
Desktop

bapred

A package for the treatment and analysis of batch effects based in…

A package for the treatment and analysis of batch effects based in high-dimensional molecular data via batch effect adjustment and addon quantile normalization. bapred implements a plot for the…

MDQC
Desktop

MDQC Mahalanobis Distance Quality Control

A package which provides a multivariate approach to evaluate the quality of an…

A package which provides a multivariate approach to evaluate the quality of an array that examines the ‘Mahalanobis distance’ of its quality attributes from those of other arrays. MDQC flags…

Harshlight
Desktop

Harshlight

A package for the automatic detection and masking of blemishes in HDONA…

A package for the automatic detection and masking of blemishes in HDONA microarray chips. Harshlight’s algorithm combines image analysis techniques with statistical approaches to recognize three…

fRMA
Desktop

fRMA

A package based on a single-array preprocessing algorithm that retains the…

A package based on a single-array preprocessing algorithm that retains the advantages of multiarray algorithms and removes certain batch effects by downweighting probes that have high between-batch…

FARMS
Desktop

FARMS Factor Analysis for Robust Microarray Summarization

A model-based technique for summarizing high-density oligonucleotide array data…

A model-based technique for summarizing high-density oligonucleotide array data at probe level for Affymetrix GeneChips.

maCorrPlot
Desktop

maCorrPlot

A package that graphically displays correlation in microarray data that is due…

A package that graphically displays correlation in microarray data that is due to insufficient normalization. maCorrPlot is based on a simple graphical method for assessing the quality of low-level…

ExpressYourself
Web

ExpressYourself

A web-based program for processing microarray data. In completely automated…

A web-based program for processing microarray data. In completely automated fashion, ExpressYourself will correct the background array signal, normalize the Cy5 and Cy3 signals, score levels of…

gprege
Desktop

gprege

A package for ranking differentially expressed gene expression time courses…

A package for ranking differentially expressed gene expression time courses through Gaussian process regression. gprege fits two GPs with the an RBF (+ noise diagonal) kernel on each profile. One GP…

XPN
Desktop

XPN

Merging Two Gene Expression Studies via Cross Platform Normalization.

Merging Two Gene Expression Studies via Cross Platform Normalization.

virtualArray
Desktop

virtualArray

Combines raw data of different microarray platforms into one virtual array.…

Combines raw data of different microarray platforms into one virtual array. virtualArray consists of several functions that act subsequently in a semi-automatic way. Doing as much of the data…

RUVnormalize
Desktop

RUVnormalize

Removes unwanted variation from gene expression data when the factor of…

Removes unwanted variation from gene expression data when the factor of interest is not defined, e.g., to clean up a dataset for general use or to do any kind of unsupervised analysis. RUVnormalize…

CALIB
Desktop

CALIB

A package for normalization of two-color microarray data. CALIB is based on the…

A package for normalization of two-color microarray data. CALIB is based on the measurements of external controls and estimates an absolute target level for each gene and condition pair, as opposed…

AffyRNADegradat…
Desktop

AffyRNADegradation

A package that assesses RNA quality of Affymetrix expression data. The…

A package that assesses RNA quality of Affymetrix expression data. The AffyRNADegradation package extends the Bioconductor package affy and integrates well in a typical microarray analysis workflow.…

EXPANDER
Desktop

EXPANDER EXpression Analyzer and DisplayER

An integrated software platform for the analysis of microarray gene expression…

An integrated software platform for the analysis of microarray gene expression data. EXPANDER is designed to support all the stages of microarray data analysis, from raw data normalization to…

BatchQC
Desktop

BatchQC

A software pipeline which addresses these issues using interactive…

A software pipeline which addresses these issues using interactive visualizations and statistics that evaluate the impact of batch effects in a genomic dataset. BatchQC can also apply existing…

R/DWD
Desktop

R/DWD

Provides the implementation of distance weighted discrimination (DWD) using an…

Provides the implementation of distance weighted discrimination (DWD) using an interior point method for the solution of second order cone programming problems. DWD is related to, and has been shown…

SVAPLS
Desktop

SVAPLS

Implements Partial Least Squares regression to extract the hidden signals of…

Implements Partial Least Squares regression to extract the hidden signals of sample-specific heterogeneity in the data and uses them to find the genes that are actually correlated with the phenotype…

VBMP
Desktop

VBMP Variational Bayesian Multinomial Probit Regression

Features multinomial probit regression with Gaussian Process priors and…

Features multinomial probit regression with Gaussian Process priors and estimates class posterior probabilities employing fast variational approximations to the full posterior. VBMP is an R package…

RefPlus
Desktop

RefPlus

Contains functions for pre-processing Affymetrix data using the RMA+ (the…

Contains functions for pre-processing Affymetrix data using the RMA+ (the Extrapolation Strategy) and the RMA++ (Extrapolation Averaging) methods. RefPlus is implemented in the R language. RMA+ is an…

Codelink
Desktop

Codelink

Performs high-throughput expression analysis, with accurate and consistent…

Performs high-throughput expression analysis, with accurate and consistent results. Codelink is a single-channel microarray platform that uses 30-bp oligonucleotide probes designed for three…

Oligo package
Desktop

Oligo package

Implements a unified framework for preprocessing microarray data and interfaces…

Implements a unified framework for preprocessing microarray data and interfaces with other BioConductor tools for downstream analysis. The Oligo package provides array coordinates, feature types,…

ComBat
Desktop

ComBat

Adjusting batch effects in microarray expression data using Empirical Bayes…

Adjusting batch effects in microarray expression data using Empirical Bayes methods. The modified ComBat (M-Combat) is designed specifically in the context of meta-analysis and batch effect…

fSVA
Desktop

fSVA frozen Surrogate Variable Analysis

Developed for prediction problems. fSVA borrows strength from a training set…

Developed for prediction problems. fSVA borrows strength from a training set for individual sample batch correction. It improves prediction accuracy in simulations and in public genomic studies. The…

Ariadne
Desktop

Ariadne

Offers reliable and automated analysis of large-scale SRM differential…

Offers reliable and automated analysis of large-scale SRM differential expression studies. To quantify monitored targets, Ariadne exploits metadata imported from the transition lists, and targets can…

TurboNorm
Desktop

TurboNorm

A package based on an intensity-dependent normalization method for microarrays…

A package based on an intensity-dependent normalization method for microarrays that is fast, simple and can include weighing of observations. TurboNorm is based on the P-spline scatterplot smoother…

PLIDA
Desktop

PLIDA

Capable of normalizing gene expression data collected on different platforms…

Capable of normalizing gene expression data collected on different platforms even when there are systematic differences between the samples on each platform.

AMEN
Desktop

AMEN Annotation Mapping Expression and Network

Enables biological and medical researchers with basic bioinformatics training…

Enables biological and medical researchers with basic bioinformatics training to manage and explore genome annotation, chromosomal mapping, protein -protein interaction (PPI), expression profiling…

Goulphar
Desktop

Goulphar

Combines and extends functions found in BioConductor packages (limma and…

Combines and extends functions found in BioConductor packages (limma and marray) to correct for dye biases and spatial artifacts. Goulphar provides a wide range of optional and customizable filters…

equalizer
Desktop

equalizer

Reduces probe hybridization bias from experiments performed on the Affymetrix…

Reduces probe hybridization bias from experiments performed on the Affymetrix microarray platform, allowing accurate assessment of germline influence on gene expression. equalizer uses genome variant…

maskBAD
Desktop

maskBAD masking BAD microarray probes

Detects and removes probes with different binding affinity in Affymetrix array…

Detects and removes probes with different binding affinity in Affymetrix array expression data. The method implemented in maskBAD performs better than other methods in detecting binding affinity…

yaqcaffy
Desktop
pvac
Desktop

pvac

Contains the function for filtering genes by the proportion of variation…

Contains the function for filtering genes by the proportion of variation accounted for by the first principal component (PVAC).

qcmetrics
Desktop

qcmetrics

Provides a framework for generic quality control of data. qcmetrics permits to…

Provides a framework for generic quality control of data. qcmetrics permits to create, manage and visualise individual or sets of quality control metrics and generate quality control reports in…

SNAGEE
Desktop
affyQCReport
Desktop

affyQCReport

A package that creates a QC report for an AffyBatch object. The report is…

A package that creates a QC report for an AffyBatch object. The report is intended to allow the user to quickly assess the quality of a set of arrays in an AffyBatch object.

arrayMvout
Desktop

arrayMvout

This package supports the application of diverse quality metrics to AffyBatch…

This package supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify…

arrayQuality
Desktop

arrayQuality

A package that assesses array quality on spotted arrays. arrayQuality offers…

A package that assesses array quality on spotted arrays. arrayQuality offers functions for performing print-run and array level quality assessment.

Beadarray
Desktop

Beadarray

Ables to read beadlevel data (raw TIFFs and text files) output by BeadScan as…

Ables to read beadlevel data (raw TIFFs and text files) output by BeadScan as well as beadsummary data from BeadStudio. Beadarray also provides methods for quality assessment and lowlevel analysis.

ffpe
Desktop

ffpe

A package that identifies low-quality data using metrics developed for…

A package that identifies low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Ffpe also offers a function for making Concordance…

affyPLM
Desktop

affyPLM

A package that extends and improves the functionality of the base affy package.…

A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting…

LMGene
Desktop

LMGene

A package for analysis of microarray data using a linear model and glog data…

A package for analysis of microarray data using a linear model and glog data transformation. LMGene allows the identification of Differentially Expressed Genes in Gene Expression Arrays.

aroma.light
Desktop

aroma.light

A package which uses light-weight methods for normalization and visualization…

A package which uses light-weight methods for normalization and visualization of microarray data using only basic R data types. These methods for microarray analysis take basic data types such as…

SCAN.UPC
Desktop

SCAN.UPC

A package Facilitates personalized-medicine workflows, based on a microarray…

A package Facilitates personalized-medicine workflows, based on a microarray normalization method. Rather than processing microarray samples as groups, which can introduce biases and present…

genArise
Desktop

genArise

An easy to use tool for dual color microarray data. genArise’s GUI-Tk based…

An easy to use tool for dual color microarray data. genArise’s GUI-Tk based environment lets any non-experienced user performs a basic, but not simple, data analysis just following a wizard. In…

nnNorm
Desktop

nnNorm

Allows to detect and correct for spatial and intensity biases with two-channel…

Allows to detect and correct for spatial and intensity biases with two-channel microarray data. The normalization method implemented in nnNorm is based on robust neural networks fitting.

PVCA
Desktop

PVCA Principal Variance Component Analysis

Contains the function to assess the batch sources by fitting all…

Contains the function to assess the batch sources by fitting all "sources" as random effects.

RAMA
Desktop

RAMA Robust Analysis of MicroArrays

Provides robust estimation of cDNA microarray intensities with replicates. RAMA…

Provides robust estimation of cDNA microarray intensities with replicates. RAMA uses a Bayesian hierarchical model for the robust estimation. Outliers are modeled explicitly using a t-distribution,…

STEPNORM
Desktop

STEPNORM

Provides a data-dependent and adaptive normalization of two-channel spotted…

Provides a data-dependent and adaptive normalization of two-channel spotted microarrays. STEPNORM performs a stepwise interrogation of a range of different normalization models and selects the…

vsn
Desktop

vsn

Implements a method for normalising microarray intensities, and works for…

Implements a method for normalising microarray intensities, and works for single- and multiple-color arrays. vsn can also be used for data from other technologies, as long as they have similar…

inSilicoMerging
Desktop

inSilicoMerging

Collection of techniques to remove inter-study bias when combining gene…

Collection of techniques to remove inter-study bias when combining gene expression data originating from different studies.

svd
Desktop

svd

Interfaces to various state-of-art SVD and eigensolvers. svd provides various R…

Interfaces to various state-of-art SVD and eigensolvers. svd provides various R bindings to various SVD and eigensolvers (PROPACK, nuTRLan).

EBS
Desktop

EBS Empirical Bayes Screening

Inspects a large number of p-values in an effort to detect additional positive…

Inspects a large number of p-values in an effort to detect additional positive cases. EBS offers an automatic screening of the p-values a user may obtain from his or her favorite gene-by-gene…

MBP
Algorithm

MBP Module-Based Prediction approach

A module-based prediction strategy via unsupervised gene clustering to overcome…

A module-based prediction strategy via unsupervised gene clustering to overcome the drawbacks of traditional gene-based prediction (GBP) models. MBP is portable to any test study as long as partial…

rGN
Desktop

rGN ratio-adjusted Gene-wise Normalization

An analytical method with equal mixture assumption for ratio-adjusted gene-wise…

An analytical method with equal mixture assumption for ratio-adjusted gene-wise normalization. rGN is developed to adjust for the imbalanced ratio effect. A calibration scheme is further suggested…

Micro-Analyzer
Desktop

Micro-Analyzer

Java tool that performs the preprocessing of Expression and SNPs microarray…

Java tool that performs the preprocessing of Expression and SNPs microarray Affymetrix.

APT
Desktop

APT Affymetrix Power Tools

A set of cross-platform command line programs that implement algorithms for…

A set of cross-platform command line programs that implement algorithms for analyzing and working with Affymetrix GeneChip arrays.

MIDAW
Web

MIDAW

Integrates a series of statistical algorithms that can be used for processing…

Integrates a series of statistical algorithms that can be used for processing and interpretation of microarray data. MIDAW consists of two main sections: (i) data normalization and (ii) data…

SIMAGE
Web

SIMAGE

Aims at validating image analysis and spot quantification and simulate…

Aims at validating image analysis and spot quantification and simulate TIF-images of the visualized spots. The SIMAGE web site consists of three parts: (i) a start page where the user may upload…

CONOR
Desktop

CONOR CrOss-platform NOrmalization in R

Normalizes gene expression data to be comparable for different microarray…

Normalizes gene expression data to be comparable for different microarray platforms. CONOR is an R package capable of performing the following nine cross-platform normalization methods:…

AffyMAPSDetector
Desktop

AffyMAPSDetector Affymetrix MicroArray Probe SNP Detector

A tool that can be used to supplement the annotations provided for probes on…

A tool that can be used to supplement the annotations provided for probes on the Affymetrix GeneChip platform. Output from this tool characterizes SNP-containing probes on GeneChip microarrays, thus…

MIDAS
Desktop

MIDAS Microarray Data Analysis System

A Java application, provides users an intuitive interface to design analysis…

A Java application, provides users an intuitive interface to design analysis protocols combining one or more normalization and filtering steps. MIDAS provides scatterplots that illustrate the effects…

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