Biocview "Microarray"

Access and Analyze DNA Methylation Array Databases

Access and analyze public DNA methylation array data compilations

Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet

Access the ArrayExpress Microarray Database at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet

A correction of the local pooled error (LPE) method to replace the asymptotic variance adjustment with an unbiased adjustment based on sample size.

A "corrective make-up" program for microarray chips

Active modules for multilayer weighted gene co-expression networks: a continuous optimization approach

ADAM: Activity and Diversity Analysis Module

Adaptive Gene Picking for Microarray Expression Data Analysis

Adaptive Robust Regression normalization for Illumina methylation data

Adjust for positional and batch effects using ComBat

A fast scatterplot smoother suitable for microarray normalization

Affected pathway ranking in differential gene expression analysis

Affymetrix-based RMA Processing Using Fixed Parameters

Affymetrix expression data quality control and reproducibility analysis

Affymetrix File Parsing SDK

Affymetrix GeneChip software compatibility

Affymetrix Quality Assessment and Analysis Tool

Affymetrix SNP Probe-Summarization using Non-Negative Matrix Factorization

Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool

A Framework for Quality Control

A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods.

A gene recommender algorithm to identify genes coexpressed with a query set of genes

A generic R plugin dispatcher for BASE

A gene-signature ranking method based on sample density in PCA space

A Genotype Calling Algorithm for Affymetrix SNP Arrays

A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops

A graphical user interface to conduct a dose-response analysis of microarray data

Agreement of Differential Expression Analysis

A Hybrid Feature Selection method for gene expression data

AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype

A k-tables approach to integrate multiple Omics-Data

Algorithms for Calculating Microarray Enrichment (ACME)

Alikeness Based on Regression on Transciptome DECOnvolution

alternative CDF environments (aka probeset mappings)

Analysis of Agilent Microarray Data [draft]

Analysis of big data from aCGH experiments using parallel computing and ff objects

Analysis of DNA methylation data from CHARM microarrays

Analysis of Illumina microarray data [A DRAFT - TRUE]

Analysis of Large Affymetrix Microarray Data Sets

Analysis of Parent-Specific DNA Copy Numbers

ANalysis Of Translational Activity (ANOTA).

Analyze and correct probe positional bias in microarray data due to RNA degradation

Analyze Illumina Infinium DNA methylation arrays

An integrated analysis package of Gene expression and Copy number alteration

An integrated analysis package of miRNA and mRNA expression data

An Interactive Consensus Clustering Framework for Multi-platform Data Analysis

Annotate microarrays and perform cross-species gene expression analyses using flat file databases

Annotate the Gene Symbols for Probes in Expression Array

Annotation and gene expression data retrieval from Bgee database

Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology

Annotation-Driven Clustering

Annotation tools for Affymetrix biological metadata

An R Object-oriented Microarray Analysis package

An R package for qualitative biclustering in support of gene co-expression analyses

An R Package for Time Course RNASeq Data Analysis

An R Package to Collect Everyones Homework

A Package for De Novo CNV Detection in Case-Parent Trios

A package for nonlinear dimension reduction with Isomap and LLE.

A Pipeline to Process RNAseq Data

Application of gene classifiers

A probe-level data file format used by aroma.affymetrix [DEPRECATED]

A Probe-Level Data File Format Used by 'aroma.affymetrix' [deprecated]

A RangedSummarizedExperiment with methods for copy number analysis

Artificial Components Detection of Differentially Expressed Genes

A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling

Assess Differential Gene Expression Experiments with ERCC Controls

Assessing array quality on spotted arrays

Assign Properties to TNBC Patients

Associates DNA Methylation with Matched gene Expression

A Systems Biology Approach for Drug Repurposing

A test for when to use quantile normalization

A time series clustering package combining slope and Frechet distances

A Tool for Generic Cell Type Enrichment Analysis

A Tool for Integration of Big Bio Data

a tool set for pathway based data integration and visualization

A tool to use GO Subtrees to Tag and Annotate Genes within a set

A user friendly R package to perform the network enrichment analysis (NEA).

A user-friendly tool for comprehensive power estimation for epigenome wide association studies (EWAS)

Automated Affymetrix Array Analysis Base Package

Automated Affymetrix Array Analysis Classification Package

Automated Affymetrix Array Analysis Core Package

Automated Affymetrix Array Analysis Preprocessing Package

Automated Affymetrix Array Analysis Reporting Package

Automated Affymetrix Array Analysis Umbrella Package

Automated functions for comparing various omic data from cbioportal.org

A web interface for gene-set enrichment analyses

A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses

Background Adjustment Using Sequence Information

Base package for enabling powerful shiny web displays of Bioconductor objects

Basic Functions for Pre-Processing Microarrays

Batch Effects Quality Control Software

Bayesian Analysis of Chip-chip experiment

Bayesian Gene eXpression

Bayesian Hierarchical Clustering

Bayesian Inference of Regulation of Transcriptional Activity

Bayesian Inference of Regulatory Influence on Expression (biRte)

Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models

Bayesian models for differential gene expression

Bayesian Piecewise Constant Regression for DNA copy number estimation

Bayesian Robust Inference for Differential Gene Expression

BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

Benchmarking of several gene network inference methods

Biclustering Analysis and Results Exploration

Bioconductor Web Interface

Biological Network Analysis

BLMA: A package for bi-level meta-analysis

Calculates Mulcom test

Calibration model for estimating absolute expression levels from microarray data

Calling aberrations for array CGH tumor profiles.

cancer outlier Gene Profile Sets

Candidate Driver Analysis

Candidate gene prioritization based on convergent evidence

Causal network analysis methods

Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms

CGHbase: Base functions and classes for arrayCGH data analysis.

CGH Micro-Array NORmalization

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

Chromosmal Aberrations Finder in Expression data

Chromosome Instability Index

Classes and Methods for "Class Comparison" Problems on Microarrays

Classes and Methods for "Class Discovery" with Microarrays or Proteomics

Classes and Methods for "Class Prediction" with Microarrays or Proteomics

Classes and Methods for Cross Validation of "Class Prediction" Algorithms

Classes and methods for cross validation of "class prediction" with microarrays or proteomics

Classes and Methods for Training and Using Binary Prediction Models

Classes and Methods to Use Genetic Algorithms for Feature Selection

Classification using generalized partial least squares

Classifier for Single-cell RNA-seq Using Cell Clusters

Classify diseases and build associated gene networks using gene expression profiles

Cluster and Tree Conversion.

Clustering of (epigenetic) DNA methylation data using a variational Bayes NMF algorithm

cn.FARMS - factor analysis for copy number estimation

coexnet: An R package to build CO-EXpression NETworks from Microarray Data

co-expressed gene-set enrichment analysis

Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis

Combination Connectivity Mapping

coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns

coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns.

CommunityAMARETTO: A Computational Tool for the Discovery of Shared and Distinct Regulatory Mechanisms Across Biological Systems

Comparison between multiple levels of gene expression

Comparison of disease and drug profiles using Gene set Enrichment Analysis

Compression of Illumina BeadArray data

Concomitant identification of distinctness and similarity in gene expression analysis.

Condition specific detection from expression data

Connect high throughput Array data from different platforms

Convert Microarray Data Objects

Convert segment data into a region by sample matrix to allow for other high level computational analyses.

Coordinated Gene Activity in Pattern Sets

Copy-Number Analysis of Large Microarray Data Sets

Copy number data analysis using DNA sequencing data

Copy number prediction with correction for GC and mappability bias for HTS data

Copy Number study and Segmentation for multivariate biological data

Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

Correlation Motif Fit

Covariate Assisted Large-scale Multiple testing

CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data

Create genotyping plate maps

Cross-platform consensus analysis of genomic measurements via interlaboratory testing method

Cross Platform Meta-Analysis of Microarray Data

Data-Adaptive Statistics for High-Dimensional Multiple Testing

Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip (USC version)

DataSHIELD client site Omics association functions.

DataSHIELD server site Omic functions

Decomposing Heterogeneous Cohorts using Omic Data Profiling

de novo motif discovery

Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM)

Detection of focal aberrations in DNA copy number data

Development and validation of diagnostic tests from high-dimensional molecular data

Differential Co-expression Analysis

Differential Expression via Distance Summary for Microarray Data

Dimension Reduction for Array CGH Data with Minimal Information Loss.

Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles

DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles

DNA copy number data analysis

DNA Copy Number Data Analysis

DNA IP-seq data analysis

DNA methylation data analysis and visualization

Dual KS Discriminant Analysis and Classification

(Dynamic) Nested Effects Models and Deterministic Effects Propagation Networks to reconstruct phenotypic hierarchies

Dynamic Transcriptome Analysis

Earth Mover's Distance for Differential Analysis of Genomics Data

Efficient algorithms for DNA methylation

Efficient and Flexible EWAS

Efficient design and analysis of factorial two-colour microarray data

ELBOW - Evaluating foLd change By the lOgit Way

Empirical Bayes estimate of block diagonal covariance matrices

Engineering Evaluation by Gene Categorization (eegc)

Enhanced copy-number variation analysis using Illumina DNA methylation arrays

Enrichment Analysis for Gene Ontology

Enrichment Approach to Predict Which Transcription Factors are Regulated

Ensemble of Gene Set Enrichment Analyses

Estimate Microarray Sample Size

Estimate the cell composition of whole blood in DNA methylation samples

Estimation of genetic and molecular regulatory networks from high-throughput genomics data

Estimation of local false discovery rate

EWCE for Multiple Gene Lists

Example experimental microarray data set for the "biotmle" R package

Exploratory analysis for two-color spotted microarray data

Expression data analysis via the Iterative Signature Algorithm

Expression Weighted Celltype Enrichment

External data sets for clustifyr

FABIA: Factor Analysis for Bicluster Acquisition

Factorial designed microarray experiment analysis

FARMS - Factor Analysis for Robust Microarray Summarization

FDR adjustments of Microarray Experiments (FDR-AME)

Feature-based association and gene-set enrichment for copy number alteration analysis in cancer

Find chromosome regions showing common gains/losses

Frozen RMA and Barcode

Frozen RMA Tools

Functionality Visualization for Motifs

Functional Network Analysis

Functions for Gene Ontology database

Functions to handle cDNA microarray data, including several methods of data analysis

Functions used to preprocess datasets stored in BioDataome

Functions useful for those doing repetitive analyses with Affymetrix GeneChips

Gain and Loss Analysis of DNA

Gaussian Process Ranking and Estimation of Gene Expression time-series

GCSscore: an R package for microarray analysis for Affymetrix/Thermo Fisher arrays

geneChip Analysis Package

Gene Expression Atlas query and gene set enrichment package.

Gene expression-based subtype classification for high-grade serous ovarian cancer

Gene expression changes in three biological conditions

Gene Expression Variation Analysis (GEVA)

genefilter: methods for filtering genes from high-throughput experiments

GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-seq data and Gene Expression Data

Generally Applicable Gene-set Enrichment for Pathway Analysis

Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq

General Sample Size and Power Analysis for Microarray and Next-Generation Sequencing Data

Generate 'BART' File

GeneRegionScan

Gene Selection

Gene set analysis following differential expression using linear (mixed) modeling with dream

Gene Set Distance Analysis (GSDA)

Gene Set Enrichment Analysis Extended to Contingency Cubes

Gene Set Regulation Index

Gene Set Variation Analysis for microarray and RNA-seq data

Gene Set Variation Analysis for Microarray and RNA-Seq Data

Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.

Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays

Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.

genotyping and copy number study tools

GEOexplorer: a webserver for gene expression analysis and visualisation

Get data from NCBI Gene Expression Omnibus (GEO)

Global test for groups of variables via model comparisons

GO-function: deriving biologcially relevant functions from statistically significant functions

goProfiles: an R package for the statistical analysis of functional profiles

Graphical user interface for OLIN

Graphics Toolbox for Assessment of Affymetrix Expression Measures

GUI for exploratory data analysis of systems biology data

GUI for limma Package with Affymetrix Microarrays

GUI for limma Package With Two Color Microarrays

Heatmaps with row and/or column covariates and colored clusters

Heterogeneous error model for identification of differentially expressed genes under multiple conditions

Hidden Variable Dynamic Modeling

Hierarchical Dependence in Meta-Analysis

HIV Annotation

Hybrid Multiple Testing

Identification and analysis of miRNA sponge interaction networks and modules

Identification and analysis of miRNA sponge regulation

Identify differentially expressed genes in microarray time-course data

Identifying Differential Effects in Tiling Microarray Data

Identifying differentially methylated regions efficiently with power and control

Identify likely duplicate samples from genomic or meta-data

Illumina 450K methylation array spatial analysis methods

Illumina 450 methylation array normalization and metrics

Illumina DNA methylation array normalization and metrics

Illumina methylation array analysis for large experiments

ImagingAMARETTO: tools for interpreting multi-omics networks for relevance to clinical outcomes and radiographic and histopathology imaging-derived biomarkers

Improved Allele-Specific Copy Number of SNP Microarrays for Downstream Segmentation

impute: Imputation for microarray data

Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure

Inference of Chromosome-length Haplotypes using Genomic Data of Single Gamete Cells

Inference of Chromosome-Length Haplotypes Using Genomic Data of Single Gamete Cells

inference of invarsion alleles from biallelic haplotype clustering

Inference on agreement between ordered lists

Inferring miRNA sponge modules in heterogeneous data

Infers biological signatures from gene expression data

Integrated Analysis on two human genomic datasets

integrated Bayesian Modeling of eQTL data

Integrating microRNA expression into signaling pathways for pathway analysis

Integration of Microarray Data for Meta-analysis

Integrative clustering of multi-type genomic data

Interactive HTML graphics

Interactive visualization for Illumina methylation arrays

Inversions in genotype data

ITALICS

JODA algorithm for quantifying gene deregulation using knowledge

KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline

L1-regularization based methods for detection of differential splicing

Landscape Expression Visualization Interface

Laplace Mixture Model in Microarray Experiments

Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types

Linear Model decomposition for Designed Multivariate Experiments

Linear Model of background subtraction and the Langmuir isotherm

Linear Models for Microarray Data

Linear Model Toolset for Gene Set Enrichment Analysis

LMGene Software for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays

Local Pooled Error Test for Differential Expression with Paired High-throughput Data

logit-t Package

LVS normalization for Agilent miRNA data

MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data

Mahalanobis Distance Quality Control for microarrays

Manipulation of Codelink microarray data

Manipulation of SQLite-based annotations in Bioconductor

Marker Gene Finder in Microarray gene expression data

masan uses bioconductor to analyze microarray data

Masking probes with binding affinity differences

massiR: MicroArray Sample Sex Identifier

Massive and Integrative Gene Set Analysis

Massive correlating biclusters for gene expression data and associated methods

Maximum Likelihood Estimation of DNA Methylation and Hydroxymethylation Proportions

MBCB (Model-based Background Correction for Beadarray)

Merge Maid

MetaAnalysis for High Throughput Experiments

Methods for Affymetrix Oligonucleotide Arrays

Methods for analyzing microarray data using Local Pooled Error (LPE) method

Methods for fitting probe-level models

Methods for Spike-in Arrays

Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape

Methylated CpGs Set Enrichment Analysis

Methylation array and sequencing spatial analysis methods

MethyLiution: A QC Pipeline For Methylation Data

MiChip Parsing and Summarizing Functions

Microarray Analysis of Differential Expression

Microarray Analysis tool

MicroArray Chromosome Analysis Tool

MicroArray Gene-expression-based Program In Error rate estimation

Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Microrarray (AB1700) gene expression data.

Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots

mimager: The Microarray Imager

MiRNA Ranking by Gene Expression

miRNAtap: microRNA Targets - Aggregated Predictions

Misclassification Penalized Posterior Classification

Missing Value Estimation of DNA Methylation Data

MODA: MOdule Differential Analysis for weighted gene co-expression network

Modeling Network State Transitions from Expression and Regulatory data (MONSTER)

Modelling Experimental Data from MeDIP Enrichment

Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their perturbation from controls

Motif Identification and Validation

Multiple Testing using SAM and Efron's Empirical Bayes Approaches

Multi sample aCGH analysis package using kernel convolution

Multivariate analysis of microarray data using ADE4

Multivariate and directional gene set testing

Multivariate Correlation Estimator and Statistical Inference Procedures.

multivariate outlier detection for expression array QA

Murine Palate miRNA Expression Analysis

Muscle Epigenetic Age Test

Mutation Order Prediction

Mutual Information NETworks

Network reverse engineering from time course data.

Normalization of array CGH data with imbalanced aberrations.

Normal Uniform Differential Gene Expression detection

Nucleosome positioning package for R

Objective Assessment of Copy-Number Estimates

Omics Data Integration Project

ontology enrichment analysis

Operating characteristics plus sample size and local fdr for microarray experiments

Optimized local intensity-dependent normalisation of two-color microarrays

Outlier detection using quantile regression on the M-A scatterplots of high-throughput data

Outlier Gene Set Analysis

Overlay omics data onto SBGN pathway diagram

PAA (Protein Array Analyzer)

Package for enabling powerful shiny web displays of Bioconductor objects

Package to work with miRNAs and miRNA targets with R

Pairwise INTegration of functional genomics data

PANDA Algorithm

Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays

Parametric Gene Set Enrichment Analysis

Parsing Illumina Microarray Output Files

PatchseqMap

PathoStat Statistical Microbiome Analysis Package

Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)

PCA-based gene filtering for Affymetrix arrays

pcaGoPromoter is used to analyze DNA micro array data

Peptide Annotation and Data Visualization using Gviz

Peptide microarray data package

Perform co-DE gene analysis

Perform methylation analysis

Perform methylation analysis and facilitates differential expression analyses

Performs differential gene expression Analysis

Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA)

Permutation-Based Confidence for Molecular Classification

Phenotype prediction using microarray data: approach of the best overall team in the IMPROVER Diagnostic Signature Challenge

Pipeline for augmented co-expression analysis

Placental DNA methylation analysis tools

Platform for integrative analysis of omics data

Plots data (continuous/discrete) along chromosomal ideogram

Plot stacked logos for single or multiple DNA, RNA and amino acid sequence

Plotting data and annotation information along genomic coordinates

Plotting genomic information from Ensembl

Post-normalization of total copy numbers

Predict genes expressed selectively in specific cell types

Predicting Targets for Drosophila Intragenic miRNAs

Prepares microarray data for submission to GEO

Pre-process DNA Copy Number (CN) Data for Detection of CN Events

Preprocessing of Illumina Infinium 450K data

Preprocessing tools for oligonucleotide arrays

Preprocessing tools for oligonucleotide arrays.

Principal Coordinates and Hotelling's T-Square method

Principal Variance Component Analysis (PVCA)

Probabilistic combinatorial nested effects model

Probe Dependent Nearest Neighbours (PDNN) for the affy package

Probe-level Expression Change Averaging

Probe level Locally moderated Weighted t-tests.

Probe region expression estimation for RNA-seq data for improved microarray comparability

Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Processing and Differential Expression Analysis of Agilent microRNA chips

Processing Various Types of Data on GEO and TCGA

Profiles and targets subpopulations with high Treatment EEFects

Projection onto Orthogonal Space Testing for High Dimensional Data

PRojection Onto the Most Interesting Statistical Evidence

PROMISE analysis with Canonical Correlation for Two Forms of High Dimensional Genetic Data

Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)

Protein Micro Array Data Management and Interactive Visualization

QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data

QC Report Generation for affyBatch objects

Quality assessment and control for FFPE microarray expression data

Quality assessment and low-level analysis for Illumina BeadArray data

Quality control and analysis tools for Illumina DNA methylation BeadChip

Quality control for target capture experiments

Quality Control of Normalized Gene Expression Data

Quality metrics and data processing methods for NanoString mRNA gene expression data

Quality metrics report for microarray data sets

Quantification of the Tumor Immune contexture from RNA-seq data

Quantify and interpret divers of variation in multilevel gene expression experiments

Quantify and interpret drivers of variation in multilevel gene expression experiments

Quantifying the accuracy of cellular deconvolution

query gene expression data and plots from BrainStars (B*)

qusage: Quantitative Set Analysis for Gene Expression

Random Rotation Methods for High Dimensional Data with Batch Structure

Rank Product method for identifying differentially expressed genes with application in meta-analysis

Rapid Reconstruction of Time-Varying Gene Regulatory Networks

RBioinf

RBM: a R package for microarray and RNA-Seq data analysis

Rcpp Integration Surrogate Variable Analysis

Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets

Regional Expression Biases

Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression

Removal of unwanted variation for gene-gene correlations and related analysis.

Repetitive Element Methylation Prediction

Reproducibility-Optimized Test Statistic

Reproducible GSEA Benchmarking

Resampling-based multiple hypothesis testing

Reversible Jump MCMC for the Analysis of CGH Arrays

R functions for the normalization of Exiqon miRNA array data

Rhythmicity Analysis Incorporating Non-parametric Methods

'rifi' analyses data from rifampicin time series created by microarray or RNAseq

R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data.

R Interface with InterMine-Powered Databases

R Investigation of ChIP-chip Oligoarrays

RNA-binding protein motif analysis

R Normalization and Inference of Time Series data

Robust Analysis of MicroArrays

Robust likelihood-based survival modeling with microarray data

R Onto-Tools suite

Routines for the functional analysis of biological networks

R package for calling CNV from Illumina 450k methylation microarrays

R package for combining multiple scans

RPA: Robust Probabilistic Averaging for probe-level analysis

runibic: row-based biclustering algorithm for analysis of gene expression data in R

Sample Classifier

Sample Size and Power Calculation in Micorarray Studies

Sample Size Calculation for RNA-Seq Experimental Design

"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"

Seamless navigation through combined results of set-based and network-based enrichment analysis

Secondary analyses of CNV data (HRD and more)

Segmentation, normalisation and processing of aCGH data

Semi-supervised adaptive-height snipping of the Hierarchical Clustering tree

Semi-Supervised Mixture Model

ShinyÉPICo

sigFeature: Significant feature selection using SVM-RFE & t-statistic

Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations

Signal-to-Noise applied to Gene Expression Experiments

Significance of periodic expression pattern in time-series data

Significant Gene Expression Profile Differences in Time Course Gene Expression Data

Similar Binding Profiles

Similarities of Ordered Gene Lists

Simple tiling array analysis of Affymetrix ChIP-chip data

simple Two-Tier Mapper: an interface for Two-Tier Mapper

Simplified RNA-Seq Analysis Pipeline

Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)

Single-Sample Classifier of Medulloblastoma Subtypes for Medulloblastoma Patient Samples, Mouse Models, and Cell Lines

Smooth quantile normalization

SnpMatrix and XSnpMatrix classes and methods

Soft clustering of time series gene expression data

Sparse Contrastive Principal Component Analysis

Spatial and intensity based normalization of cDNA microarray data based on robust neural nets

spatialHeatmap

spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions

Sscore2: an R package for microarray analysis for Affymetrix/Thermo Fisher arrays

Statistical Analysis for Developmental Microarray Time Course Data

Statistical analysis of peptide microarrays

Statistical Analysis of the GeneChip

Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD)

Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)

Statistics for Integrative Genomics Analyses in R

Stepwise Classification of Cancer Samples using High-dimensional Data Sets

Stepwise normalization functions for cDNA microarrays

Summarization and expression/phenotype association of CNV ranges

SuperCurve RPPA Sample Data

Supervised Normalization of Microarrays

Supporting Data Simulation R-package for quantro

Surrogate Variable Analysis

Survival analysis for gene signatures

Synthetic Expression Data for Gene Regulatory Network Inference

Targeted Learning with Moderated Statistics for Biomarker Discovery

Testing Groups of Covariates/Features for Association with a Response Variable, with Applications to Gene Set Testing

Testing of SNPs and SNP Interactions in Case-Parent Trio Studies

The Bimodality Index

The Discordant Method: A Novel Approach for Differential Correlation

The GASSCO method for correcting for slide-dependent gene-specific dye bias

The Genomic STate ANnotation Package

The Iterative Bayesian Model Averaging (BMA) algorithm

The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis

The removal of batch effects from datasets using a PCA and constrained optimisation based technique

The 'snp.matrix' and 'X.snp.matrix' Classes

This package is designed to perform Gene Set Analysis across multiple genomic platforms

This package was built to cluster gene expression data using the Gaussian Infinite Mixture Model.

Time-Course Multi-Omics data integration

Tool for Evaluation of Cell Identity from Transcription Profiles

Tools for analyzing Micro Array experiments

Tools for Connectivity Map-like analyses

Tools for curating, analyzing, and manipulating biological sequences

Tools for Genome Wide Association Studies

Tools for HELP data analysis

Tools for making reports in various formats

Tools for manipulating GO and microarrays

Tools for microbiome analysis

Tools for parsing Affymetrix data files

Tools for the analysis of heterogeneous tissues

Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level

Tools to test association between gene expression and phenotype in a way that is efficient, structured, fast and scalable. We also provide tools to do GSEA (Gene set enrichment analysis) and copy number variation.

Top Scoring Pairs for Microarray Classification

Transcriptional analysis based on transcriptograms

Transcriptional Regulatory Inference from Genetics of Gene ExpRession

Transcription factor Inference through Gaussian process Reconstruction of Expression

Transcript mapping with high-density oligonucleotide tiling arrays

Transcriptome instability analysis

Transcriptomic Ovarian Cancer Datasets

Two-sample tests on a graph

Two-Tier Mapper: a clustering tool based on topological data analysis

Unified methods for the inference and analysis of gene regulatory networks

Unified Statistical Modeling of Omics Data

Utilities to compute, compare, and plot the agreement between ordered vectors of features (ie. distinct genomic experiments). The package includes Correspondence-At-the-TOP (CAT) analysis.

Variance stabilization and calibration for microarray data

Variance stabilization in flow cytometry (and microarrays)

Very simple high level analysis of Affymetrix data

Visual and interactive gene expression analysis

Visual and interactive quality control of large Illumina DNA Methylation array data sets

Visualise microarray and RNAseq data using gene ontology annotations

Visualize artificial correlation in microarray data

Visualize biclusters identified in gene expression data

Wavelet-Based Models for Tiling Array Transcriptome Analysis

waveTiling Example Data

XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression

Biocview "Microarray"

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