Biocview "TwoChannel"

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

Adaptive Robust Regression normalization for Illumina methylation data

A fast scatterplot smoother suitable for microarray normalization

Affymetrix SNP Probe-Summarization using Non-Negative Matrix Factorization

A generic R plugin dispatcher for BASE

Analysis of Agilent Microarray Data [draft]

Analysis of Illumina microarray data [A DRAFT - TRUE]

Analysis of Parent-Specific DNA Copy Numbers

Analyze Illumina Infinium DNA methylation arrays

Annotate the Gene Symbols for Probes in Expression Array

An R Object-oriented Microarray Analysis package

A Pipeline to Process RNAseq Data

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

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

Assessing array quality on spotted arrays

Bayesian Robust Inference for Differential Gene Expression

BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

Calibration model for estimating absolute expression levels from microarray data

CGH Micro-Array NORmalization

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

Convert Microarray Data Objects

Copy-Number Analysis of Large Microarray Data Sets

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

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

Differential Co-expression Analysis

Efficient algorithms for DNA methylation

Efficient design and analysis of factorial two-colour microarray data

ELBOW - Evaluating foLd change By the lOgit Way

Ensemble of Gene Set Enrichment Analyses

Exploratory analysis for two-color spotted microarray data

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

Functions to perform cancer outlier profile analysis.

Generally Applicable Gene-set Enrichment for Pathway Analysis

Gene regulator enrichment analysis

Get data from NCBI Gene Expression Omnibus (GEO)

Graphical user interface for OLIN

GUI for limma Package With Two Color Microarrays

Handle Illumina methylation 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

Interactive visualization for Illumina methylation arrays

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

Linear Model decomposition for Designed Multivariate Experiments

Linear Models for Microarray Data

LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

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

Maximum Likelihood Estimation of DNA Methylation and Hydroxymethylation Proportions

Methylated CpGs Set Enrichment Analysis

Methylation array and sequencing spatial analysis methods

MethyLiution: A QC Pipeline For Methylation Data

Microarray Analysis of Differential Expression

Microarray Analysis tool

Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots

Murine Palate miRNA Expression Analysis

Normalization and reporting of Illumina SNP bead arrays

Normal Uniform Differential Gene Expression detection

Optimized local intensity-dependent normalisation of two-color microarrays

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

Permutation-Based Confidence for Molecular Classification

Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

Preprocessing of Illumina Infinium 450K data

Preprocessing tools for oligonucleotide arrays

Preprocessing tools for oligonucleotide arrays.

Probe level Locally moderated Weighted t-tests.

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

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

Quality control and analysis tools for Illumina DNA methylation BeadChip

Quality metrics report for microarray data sets

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

Repetitive Element Methylation Prediction

R functions for the normalization of Exiqon miRNA array data

R Investigation of ChIP-chip Oligoarrays

RnBeads

Robust Analysis of MicroArrays

Segmentation, normalisation and processing of aCGH data

Signal-to-Noise applied to Gene Expression Experiments

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

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

Statistical Characterization of Post-translational Modifications

Stepwise normalization functions for cDNA microarrays

Supervised Normalization of Microarrays

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

Tools for HELP data analysis

Variance stabilization and calibration for microarray data

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

Visualization of highly multiplexed imaging data in R

Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip

Biocview "TwoChannel"

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