Biocview "OneChannel"

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 "corrective make-up" program for microarray chips

A fast scatterplot smoother suitable for microarray normalization

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

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

A generic R plugin dispatcher for BASE

A Genotype Calling Algorithm for Affymetrix SNP Arrays

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

alternative CDF environments (aka probeset mappings)

Analysis of Agilent Microarray Data [draft]

Analysis of Illumina microarray data [A DRAFT - TRUE]

Analysis of Large Affymetrix Microarray Data Sets

Analysis of Parent-Specific DNA Copy Numbers

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

Annotate the Gene Symbols for Probes in Expression Array

Annotation tools for Affymetrix biological metadata

An R Object-oriented Microarray Analysis package

A package for the clinical proteomic profiling data analysis

A Pipeline to Process RNAseq Data

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

Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q, B and CV instrinsic calculations

Background Adjustment Using Sequence Information

Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models

Bayesian Robust Inference for Differential Gene Expression

BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

Bioconductor Web Interface

CDF Environment Maker

Chromosmal Aberrations Finder in Expression data

Connect high throughput Array data from different platforms

Copy-Number Analysis of Large Microarray Data Sets

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

Create Copy-Number Plots using karyoploteR functionality

Cross Platform Meta-Analysis of Microarray Data

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

Differential Co-expression Analysis

Differential expression using kernel-based score test

ELBOW - Evaluating foLd change By the lOgit Way

Ensemble of Gene Set Enrichment Analyses

EWCE for Multiple Gene Lists

Expression Weighted Celltype Enrichment

Functionality to Read and Manipulate SomaLogic ADAT files

Functions to perform cancer outlier profile analysis.

Functions useful for those doing repetitive analyses with Affymetrix GeneChips

GaGa hierarchical model for high-throughput data analysis

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

geneChip Analysis Package

Generally Applicable Gene-set Enrichment for Pathway Analysis

GeneRegionScan

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

Get data from NCBI Gene Expression Omnibus (GEO)

Global test for groups of variables via model comparisons

Graphics Toolbox for Assessment of Affymetrix Expression Measures

GUI for limma Package with Affymetrix Microarrays

Illumina 450K methylation array spatial analysis methods

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

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

LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

LVS normalization for Agilent miRNA data

Manipulation of Codelink microarray data

Maximum Likelihood Estimation of DNA Methylation and Hydroxymethylation Proportions

Methods for Affymetrix Oligonucleotide Arrays

Methods for fitting probe-level models

Methylation array and sequencing spatial analysis methods

Microarray Analysis of Differential Expression

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

Multivariate and directional gene set testing

PAA (Protein Array Analyzer)

PatchseqMap

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

PCA-based gene filtering for Affymetrix arrays

Permutation-Based Confidence for Molecular Classification

Phytoplankton Population Identification using Cell Pigmentation and/or Complexity

Plot customizable linear genomes displaying arbitrary data

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

Preprocessing tools for oligonucleotide arrays

Preprocessing tools for oligonucleotide arrays.

Probe Dependent Nearest Neighbours (PDNN) for the affy package

Probe level Locally moderated Weighted t-tests.

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

PRojection Onto the Most Interesting Statistical Evidence

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 low-level analysis for Illumina BeadArray data

Quality control and analysis tools for Illumina DNA methylation BeadChip

Quality metrics report for microarray data sets

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

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

R functions for the normalization of Exiqon miRNA array data

Signal-to-Noise applied to Gene Expression Experiments

Simple tiling array analysis of Affymetrix ChIP-chip data

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

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

Statistical Analysis of the GeneChip

Statistical Characterization of Post-translational Modifications

Supervised Normalization of Microarrays

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

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

Transcript mapping with high-density oligonucleotide tiling arrays

Transcriptomic Ovarian Cancer Datasets

Variance stabilization and calibration for microarray data

Very simple high level analysis of Affymetrix data

Visualization of highly multiplexed imaging data in R

Biocview "OneChannel"

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