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 File Parsing SDK
Affymetrix GeneChip software compatibility
Affymetrix Quality Assessment and Analysis Tool
Affymetrix SNP Probe-Summarization using Non-Negative Matrix Factorization
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 Large Affymetrix Microarray Data Sets
Analysis of Parent-Specific DNA Copy Numbers
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
A Pipeline to Process RNAseq Data
Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)
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
Copy-Number Analysis of Large Microarray Data Sets
Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework
Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework
Create Copy-Number Plots using karyoploteR functionality
Create Copy-Number Plots using karyoploteR functionality
Cross Platform Meta-Analysis of Microarray Data
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 Co-expression Analysis
Differential expression using kernel-based score test
ELBOW - Evaluating foLd change By the lOgit Way
Ensemble of Gene Set Enrichment Analyses
Ensemble of Gene Set Enrichment Analyses
EWCE for Multiple Gene Lists
Expression Weighted Celltype Enrichment
Expression Weighted Celltype Enrichment
Functionality to Read and Manipulate SomaLogic ADAT files
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
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
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)
Get data from NCBI Gene Expression Omnibus (GEO)
Get data from NCBI Gene Expression Omnibus (GEO)
Get data from NCBI Gene Expression Omnibus (GEO)
Global test for groups of variables via model comparisons
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
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
Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types
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 Models for Microarray Data
Linear Models for Microarray Data
LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments
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
Maximum Likelihood Estimation of DNA Methylation and Hydroxymethylation Proportions
Methods for Affymetrix Oligonucleotide Arrays
Methods for Affymetrix Oligonucleotide Arrays
Methods for fitting probe-level models
Methylation array and sequencing spatial analysis methods
Methylation array and sequencing spatial analysis methods
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
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
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
Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling
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
Preprocessing tools for oligonucleotide arrays
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 assessment and low-level analysis for Illumina BeadArray data
Quality control and analysis tools for Illumina DNA methylation BeadChip
Quality control and analysis tools for Illumina DNA methylation BeadChip
Quality metrics report for microarray data sets
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
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
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
Statistical Characterization of Post-translational Modifications
Supervised Normalization of Microarrays
Supervised Normalization of Microarrays
Testing Groups of Covariates/Features for Association with a Response Variable, with Applications to Gene Set Testing
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
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
Visualization of highly multiplexed imaging data in R
Visualization of highly multiplexed imaging data in R