Biocview "OneChannel"

Access the ArrayExpress Microarray Database at EBI 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 "corrective make-up" program for microarray chips
A fast scatterplot smoother suitable for microarray normalization
A fast scatterplot smoother suitable for microarray normalization
Affymetrix expression data quality control and reproducibility analysis
Affymetrix expression data quality control and reproducibility analysis
Affymetrix File Parsing SDK
Affymetrix File Parsing SDK
Affymetrix File Parsing SDK
Affymetrix GeneChip software compatibility
Affymetrix GeneChip software compatibility
Affymetrix Quality Assessment and Analysis Tool
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 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 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 interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops
alternative CDF environments (aka probeset mappings)
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
Analyze and correct probe positional bias in microarray data due to RNA degradation
Annotation tools for Affymetrix biological metadata
Annotation tools for Affymetrix biological metadata
An R Object-oriented Microarray Analysis package
A package for the clinical proteomic profiling data analysis
A package for the clinical proteomic profiling data analysis
Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q, B and CV instrinsic calculations
Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q, B and CV instrinsic calculations
Background Adjustment Using Sequence Information
Background Adjustment Using Sequence Information
Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models
Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models
Bayesian Robust Inference for Differential Gene Expression
Bayesian Robust Inference for Differential Gene Expression
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
Bioconductor Web Interface
Bioconductor Web Interface
Calculates a global test for differential gene expression between groups
Calculates a global test for differential gene expression between groups
CDF Environment Maker
CDF Environment Maker
Chromosmal Aberrations Finder in Expression data
Chromosmal Aberrations Finder in Expression data
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
Cross Platform Meta-Analysis of Microarray Data
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
Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip
Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip
Differential Co-expression Analysis
ELBOW - Evaluating foLd change By the lOgit Way
ELBOW - Evaluating foLd change By the lOgit Way
Ensemble of Gene Set Enrichment Analyses
Ensemble of Gene Set Enrichment Analyses
Ensemble of Gene Set Enrichment Analyses
Expression Weighted Celltype Enrichment
Expression Weighted Celltype Enrichment
Expression Weighted Celltype Enrichment
Functionality to Read and Manipulate SomaLogic ADAT files
Functionality to Read and Manipulate SomaLogic ADAT files
Functionality to Read and Manipulate SomaLogic ADAT files
Functions to perform cancer outlier profile analysis.
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
Functions useful for those doing repetitive analyses with Affymetrix GeneChips
GaGa hierarchical model for high-throughput data analysis
GaGa hierarchical model for high-throughput data analysis
geneChip Analysis Package
geneChip Analysis Package
Generally Applicable Gene-set Enrichment for Pathway Analysis
Generally Applicable Gene-set Enrichment for Pathway Analysis
GeneRegionScan
GeneRegionScan
Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.
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)
Get data from NCBI Gene Expression Omnibus (GEO)
Graphics Toolbox for Assessment of Affymetrix Expression Measures
Graphics Toolbox for Assessment of Affymetrix Expression Measures
GUI for limma package with Affymetrix microarrays
GUI for limma package with Affymetrix microarrays
Illumina 450K methylation array spatial analysis methods
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
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
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 decomposition for Designed Multivariate Experiments
Linear Model of background subtraction and the Langmuir isotherm
Linear Model of background subtraction and the Langmuir isotherm
Linear Models for Microarray Data
Linear Models for Microarray Data
Linear Models for Microarray Data
LVS normalization for Agilent miRNA data
LVS normalization for Agilent miRNA data
Manipulation of Codelink microarray data
Manipulation of Codelink microarray data
Maximum Likelihood Estimation of DNA Methylation and Hydroxymethylation Levels
Methods for Affymetrix Oligonucleotide Arrays
Methods for Affymetrix Oligonucleotide Arrays
Methods for fitting probe-level models
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.
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)
PAA (Protein Array Analyzer)
Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)
Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)
PCA-based gene filtering for Affymetrix arrays
PCA-based gene filtering for Affymetrix arrays
Permutation-Based Confidence for Molecular Classification
Permutation-Based Confidence for Molecular Classification
Plot customizable linear genomes displaying arbitrary data
Plot customizable linear genomes displaying arbitrary data
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 Dependent Nearest Neighbours (PDNN) for the affy package
Probe level Locally moderated Weighted t-tests.
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 Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays
Processing and Differential Expression Analysis of Agilent microRNA chips
Processing and Differential Expression Analysis of Agilent microRNA chips
PRojection Onto the Most Interesting Statistical Evidence
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)
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
QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data
QC Report Generation for affyBatch objects
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 assessment and low-level analysis for Illumina BeadArray data
Quality assessment and low-level analysis for Illumina BeadArray data
Quality metrics report for microarray data sets
Quality metrics report for microarray data sets
Quality metrics report for microarray data sets
query gene expression data and plots from BrainStars (B*)
query gene expression data and plots from BrainStars (B*)
R functions for the normalization of Exiqon miRNA array data
R functions for the normalization of Exiqon miRNA array data
Signal-to-Noise applied to Gene Expression Experiments
Signal-to-Noise applied to Gene Expression Experiments
Simple tiling array analysis of Affymetrix ChIP-chip data
Simple tiling array analysis of Affymetrix ChIP-chip data
Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
Statistical Analysis of the GeneChip
Statistical Analysis of the GeneChip
Supervised Normalization of Microarrays
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
Transcript mapping with high-density oligonucleotide tiling arrays
Variance stabilization and calibration for microarray data
Variance stabilization and calibration for microarray data
Very simple high level analysis of Affymetrix data
Very simple high level analysis of Affymetrix data