Bioconductor Packages

Adaptive Robust Regression normalization for Illumina methylation data

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

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

Methylation array and sequencing spatial analysis methods

Quality control and analysis tools for Illumina DNA methylation BeadChip

R functions for the normalization of Exiqon miRNA array data

Get data from NCBI Gene Expression Omnibus (GEO)

Tools for HELP data analysis

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

CGH Micro-Array NORmalization

Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)

LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

Statistical Characterization of Post-translational Modifications

MSstats GUI for Statistical Anaylsis of Proteomics Experiments

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

Optimized local intensity-dependent normalisation of two-color microarrays

Graphical user interface for OLIN

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

Repetitive Element Methylation Prediction

Gene regulator enrichment analysis

RnBeads

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

Signal-to-Noise applied to Gene Expression Experiments

A fast scatterplot smoother suitable for microarray normalization

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

Quality metrics report for microarray data sets

Illumina methylation array analysis for large experiments

Convert Microarray Data Objects

Functions to perform cancer outlier profile analysis.

Visualization of highly multiplexed imaging data in R

An interactive multi-channel image viewer for R

Efficient design and analysis of factorial two-colour microarray data

Differential Co-expression Analysis

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

Generally Applicable Gene-set Enrichment for Pathway Analysis

Microarray Analysis tool

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

Linear Models for Microarray and Omics Data

GUI for limma Package With Two Color Microarrays

Linear Model decomposition for Designed Multivariate Experiments

BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

Methylated CpGs Set Enrichment Analysis

Exploratory analysis for two-color spotted microarray data

Handle Illumina methylation data

Analyze Illumina Infinium DNA methylation arrays

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

Preprocessing of Illumina Infinium 450K data

Preprocessing tools for oligonucleotide arrays

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

Rotation based gene set analysis