Biocview "Microarray"

Access and analyze the Recount Methylation database
Access the ArrayExpress Microarray Database at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet
A correction of the local pooled error (LPE) method to replace the asymptotic variance adjustment with an unbiased adjustment based on sample size.
A "corrective make-up" program for microarray chips
Active modules for multilayer weighted gene co-expression networks: a continuous optimization approach
Active modules for multilayer weighted gene co-expression networks: a continuous optimization approach
Adaptive Gene Picking for Microarray Expression Data Analysis
Adaptive Robust Regression normalization for Illumina methylation data
Adjust for positional and batch effects using ComBat
Adjust for positional and batch effects using ComBat
A fast scatterplot smoother suitable for microarray normalization
Affected pathway ranking in differential gene expression analysis
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
Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool
A Framework for Quality Control
A Framework for Quality Control
A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods.
A gene recommender algorithm to identify genes coexpressed with a query set of genes
A generic R plugin dispatcher for BASE
A gene-signature ranking method based on sample density in PCA space
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 user interface to conduct a dose-response analysis of microarray data
A graphical user interface to conduct a dose-response analysis of microarray data
Agreement of Differential Expression Analysis
A Hybrid Feature Selection method for gene expression data
A Hybrid Feature Selection method for gene expression data
AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype
A k-tables approach to integrate multiple Omics-Data
A k-tables approach to integrate multiple Omics-Data
Algorithms for Calculating Microarray Enrichment (ACME)
Alikeness based on Regression on Transciptome DECOnvolution
Alikeness based on Regression on Transciptome DECOnvolution
alternative CDF environments (aka probeset mappings)
Analysis of Agilent Microarray Data [draft]
Analysis of big data from aCGH experiments using parallel computing and ff objects
Analysis of DNA methylation data from CHARM microarrays
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
ANalysis Of Translational Activity (ANOTA).
Analyze and correct probe positional bias in microarray data due to RNA degradation
Analyze Illumina Infinium DNA methylation arrays
Analyze Illumina Infinium DNA methylation arrays
Analyze Illumina Infinium DNA methylation arrays
An integrated analysis package of Gene expression and Copy number alteration
An integrated analysis package of miRNA and mRNA expression data
An integrated analysis package of miRNA and mRNA expression data
An Interactive Consensus Clustering Framework for Multi-platform Data Analysis
An Interactive Consensus Clustering Framework for Multi-platform Data Analysis
Annotate microarrays and perform cross-species gene expression analyses using flat file databases
Annotate microarrays and perform cross-species gene expression analyses using flat file databases
Annotation and gene expression data retrieval from Bgee database
Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology
Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology
Annotation-Driven Clustering
Annotation tools for Affymetrix biological metadata
An R Object-oriented Microarray Analysis package
An R package for qualitative biclustering in support of gene co-expression analyses
A Package for De Novo CNV Detection in Case-Parent Trios
A Package for De Novo CNV Detection in Case-Parent Trios
A package for nonlinear dimension reduction with Isomap and LLE.
A package for nonlinear dimension reduction with Isomap and LLE.
Application of gene classifiers
Application of gene classifiers
A probe-level data file format used by aroma.affymetrix [DEPRECATED]
A Probe-Level Data File Format Used by 'aroma.affymetrix' [deprecated]
A Probe-Level Data File Format Used by 'aroma.affymetrix' [deprecated]
A RangedSummarizedExperiment with methods for copy number analysis
Artificial Components Detection of Differentially Expressed Genes
A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling
Assess Differential Gene Expression Experiments with ERCC Controls
Assess Differential Gene Expression Experiments with ERCC Controls
Assess Differential Gene Expression Experiments with ERCC Controls
Assess Differential Gene Expression Experiments with ERCC Controls
Assessing array quality on spotted arrays
Assign Properties to TNBC Patients
Assign Properties to TNBC Patients
A Systems Biology Approach for Drug Repurposing
A test for when to use quantile normalization
A test for when to use quantile normalization
A time series clustering package combining slope and Frechet distances
A time series clustering package combining slope and Frechet distances
A Tool for Integration of Big Bio Data
a tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
A tool to use GO Subtrees to Tag and Annotate Genes within a set
A tool to use GO Subtrees to Tag and Annotate Genes within a set
A user friendly R package to perform the network enrichment analysis (NEA).
A user-friendly tool for comprehensive power estimation for epigenome wide association studies (EWAS)
A user-friendly tool for comprehensive power estimation for epigenome wide association studies (EWAS)
Automated Affymetrix Array Analysis Base Package
Automated Affymetrix Array Analysis Classification Package
Automated Affymetrix Array Analysis Core Package
Automated Affymetrix Array Analysis Preprocessing Package
Automated Affymetrix Array Analysis Reporting Package
Automated Affymetrix Array Analysis Umbrella Package
A web interface for gene-set enrichment analyses
Background Adjustment Using Sequence Information
Base package for enabling powerful shiny web displays of Bioconductor objects
Base package for enabling powerful shiny web displays of Bioconductor objects
Base package for enabling powerful shiny web displays of Bioconductor objects
Basic Functions for Pre-Processing Microarrays
Basic Functions for Pre-Processing Microarrays
Batch Effects Quality Control Software
Bayesian Analysis of Chip-chip experiment
Bayesian Gene eXpression
Bayesian Hierarchical Clustering
Bayesian Inference of Regulation of Transcriptional Activity
Bayesian Inference of Regulatory Influence on Expression (biRte)
Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models
Bayesian models for differential gene expression
Bayesian Piecewise Constant Regression for DNA copy number estimation
Bayesian Piecewise Constant Regression for DNA copy number estimation
Bayesian Robust Inference for Differential Gene Expression
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
Benchmarking of several gene network inference methods
Benchmarking of several gene network inference methods
Benchmarking of several gene network inference methods
Biclustering Analysis and Results Exploration
Bioconductor Web Interface
Biological Network Analysis
Biological Network Analysis
BLMA: A package for bi-level meta-analysis
BLMA: A package for bi-level meta-analysis
Calculates Mulcom test
Calibration model for estimating absolute expression levels from microarray data
Calling aberrations for array CGH tumor profiles.
Calling aberrations for array CGH tumor profiles.
cancer outlier Gene Profile Sets
Candidate gene prioritization based on convergent evidence
Candidate gene prioritization based on convergent evidence
Candidate gene prioritization based on convergent evidence
Candidate gene prioritization based on convergent evidence
Causal network analysis methods
Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms
Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms
CGHbase: Base functions and classes for arrayCGH data analysis.
CGHbase: Base functions and classes for arrayCGH data analysis.
CGH Micro-Array NORmalization
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
Chromosmal Aberrations Finder in Expression data
Chromosome Instability Index
Classes and Methods for "Class Comparison" Problems on Microarrays
Classes and Methods for "Class Comparison" Problems on Microarrays
Classes and Methods for "Class Discovery" with Microarrays or Proteomics
Classes and Methods for "Class Discovery" with Microarrays or Proteomics
Classes and Methods for "Class Prediction" with Microarrays or Proteomics
Classes and Methods for Cross Validation of "Class Prediction" Algorithms
Classes and Methods for Cross Validation of "Class Prediction" Algorithms
Classes and methods for cross validation of "class prediction" with microarrays or proteomics
Classes and Methods for Training and Using Binary Prediction Models
Classes and Methods for Training and Using Binary Prediction Models
Classes and Methods to Use Genetic Algorithms for Feature Selection
Classes and Methods to Use Genetic Algorithms for Feature Selection
Classification using generalized partial least squares
Classification using generalized partial least squares
Classifier for Single-cell RNA-seq Using Cell Clusters
Classifier for Single-cell RNA-seq Using Cell Clusters
Classifier for Single-cell RNA-seq Using Cell Clusters
Classifier for Single-cell RNA-seq Using Cell Clusters
Classifier for Single-cell RNA-seq Using Cell Clusters
Classify diseases and build associated gene networks using gene expression profiles
Cluster and Tree Conversion.
Clustering of (epigenetic) DNA methylation data using a variational Bayes NMF algorithm
cn.FARMS - factor analysis for copy number estimation
cn.FARMS - factor analysis for copy number estimation
coexnet: An R package to build CO-EXpression NETworks from Microarray Data
coexnet: An R package to build CO-EXpression NETworks from Microarray Data
coexnet: An R package to build CO-EXpression NETworks from Microarray Data
co-expressed gene-set enrichment analysis
co-expressed gene-set enrichment analysis
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis
Combination Connectivity Mapping
Combination Connectivity Mapping
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns.
CommunityAMARETTO: A Computational Tool for the Discovery of Shared and Distinct Regulatory Mechanisms Across Biological Systems
Comparison between multiple levels of gene expression
Comparison of disease and drug profiles using Gene set Enrichment Analysis
Comparison of disease and drug profiles using Gene set Enrichment Analysis
Compression of Illumina BeadArray data
Concomitant identification of distinctness and similarity in gene expression analysis.
Condition specific detection from expression data
Connect high throughput Array data from different platforms
Convert Microarray Data Objects
Convert segment data into a region by sample matrix to allow for other high level computational analyses.
Coordinated Gene Activity in Pattern Sets
Coordinated Gene Activity in Pattern Sets
Copy-Number Analysis of Large Microarray Data Sets
Copy-Number Analysis of Large Microarray Data Sets
Copy number data analysis using DNA sequencing data
Copy number prediction with correction for GC and mappability bias for HTS data
Copy number prediction with correction for GC and mappability bias for HTS data
Copy number prediction with correction for GC and mappability bias for HTS data
Copy Number study and Segmentation for multivariate biological data
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
Correlation Motif Fit
Covariate Assisted Large-scale Multiple testing
Covariate Assisted Large-scale Multiple testing
CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data
CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data
Create genotyping plate maps
Cross-platform consensus analysis of genomic measurements via interlaboratory testing method
Cross-platform consensus analysis of genomic measurements via interlaboratory testing method
Cross Platform Meta-Analysis of Microarray Data
Cross Platform Meta-Analysis of Microarray Data
Data-Adaptive Statistics for High-Dimensional Multiple Testing
Data-Adaptive Statistics for High-Dimensional Multiple Testing
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 (USC version)
DataSHIELD client site Omics association functions.
DataSHIELD server site Omic functions.
Decomposing Heterogeneous Cohorts using Omic Data Profiling
Decomposing Heterogeneous Cohorts using Omic Data Profiling
de novo motif discovery
de novo motif discovery
Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM)
Detection of focal aberrations in DNA copy number data
Development and validation of diagnostic tests from high-dimensional molecular data
Differential Co-expression Analysis
Differential Co-expression Analysis
Differential Expression via Distance Summary for Microarray Data
Dimension Reduction for Array CGH Data with Minimal Information Loss.
Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles
DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles
DNA copy number data analysis
DNA copy number data analysis
DNA IP-seq data analysis
DNA IP-seq data analysis
DNA IP-seq data analysis
DNA IP-seq data analysis
DNA IP-seq data analysis
DNA methylation data analysis and visualization
Dual KS Discriminant Analysis and Classification
(Dynamic) Nested Effects Models and Deterministic Effects Propagation Networks to reconstruct phenotypic hierarchies
Dynamic Transcriptome Analysis
Earth Mover's Distance for Differential Analysis of Genomics Data
Earth Mover's Distance for Differential Analysis of Genomics Data
Efficient algorithms for DNA methylation
Efficient and Flexible EWAS
Efficient design and analysis of factorial two-colour microarray data
ELBOW - Evaluating foLd change By the lOgit Way
Empirical Bayes estimate of block diagonal covariance matrices
Empirical Bayes estimate of block diagonal covariance matrices
Engineering Evaluation by Gene Categorization (eegc)
Engineering Evaluation by Gene Categorization (eegc)
Enhanced copy-number variation analysis using Illumina DNA methylation arrays
Enrichment Analysis for Gene Ontology
Enrichment Analysis for Gene Ontology
Ensemble of Gene Set Enrichment Analyses
Ensemble of Gene Set Enrichment Analyses
Estimate Microarray Sample Size
Estimate the cell composition of whole blood in DNA methylation samples
Estimate the cell composition of whole blood in DNA methylation samples
Estimation of genetic and molecular regulatory networks from high-throughput genomics data
Estimation of genetic and molecular regulatory networks from high-throughput genomics data
Estimation of local false discovery rate
Example experimental microarray data set for the "biotmle" R package
Exploratory analysis for two-color spotted microarray data
Expression data analysis via the Iterative Signature Algorithm
Expression Weighted Celltype Enrichment
Expression Weighted Celltype Enrichment
External data sets for clustifyr
FABIA: Factor Analysis for Bicluster Acquisition
Factorial designed microarray experiment analysis
FARMS - Factor Analysis for Robust Microarray Summarization
FDR adjustments of Microarray Experiments (FDR-AME)
Feature-based association and gene-set enrichment for copy number alteration analysis in cancer
Find chromosome regions showing common gains/losses
Frozen RMA and Barcode
Frozen RMA and Barcode
Frozen RMA Tools
Frozen RMA Tools
Functionality Visualization for Motifs
Functional Network Analysis
Functional Network Analysis
Functions for Gene Ontology database
Functions to handle cDNA microarray data, including several methods of data analysis
Functions used to preprocess datasets stored in BioDataome
Functions useful for those doing repetitive analyses with Affymetrix GeneChips
Functions useful for those doing repetitive analyses with Affymetrix GeneChips
Gain and Loss Analysis of DNA
Gaussian Process Ranking and Estimation of Gene Expression time-series
Gaussian Process Ranking and Estimation of Gene Expression time-series
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
Gene Expression Atlas query and gene set enrichment package.
Gene expression-based subtype classification for high-grade serous ovarian cancer
Gene expression-based subtype classification for high-grade serous ovarian cancer
Gene expression changes in three biological conditions
Gene expression changes in three biological conditions
genefilter: methods for filtering genes from high-throughput experiments
genefilter: methods for filtering genes from high-throughput experiments
GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-seq data and Gene Expression Data
GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-seq data and Gene Expression Data
Generally Applicable Gene-set Enrichment for Pathway Analysis
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq
General Sample Size and Power Analysis for Microarray and Next-Generation Sequencing Data
Generate 'BART' File
Generate 'BART' File
Generate 'BART' File
GeneRegionScan
Gene Selection
Gene Set Enrichment Analysis Extended to Contingency Cubes
Gene Set Regulation Index
Gene Set Variation Analysis for microarray and RNA-seq data
Gene Set Variation Analysis for microarray and RNA-seq data
Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
genotyping and copy number study tools
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
GO-function: deriving biologcially relevant functions from statistically significant functions
goProfiles: an R package for the statistical analysis of functional profiles
goProfiles: an R package for the statistical analysis of functional profiles
Graphical user interface for OLIN
Graphics Toolbox for Assessment of Affymetrix Expression Measures
GUI for exploratory data analysis of systems biology data
GUI for exploratory data analysis of systems biology data
GUI for limma Package with Affymetrix Microarrays
GUI for limma Package With Two Color Microarrays
Heatmaps with row and/or column covariates and colored clusters
Heatmaps with row and/or column covariates and colored clusters
Heterogeneous error model for identification of differentially expressed genes under multiple conditions
Hidden Variable Dynamic Modeling
Hierarchical Dependence in Meta-Analysis
HIV Annotation
Hybrid Multiple Testing
Identification and analysis of miRNA sponge interaction networks and modules
Identification and analysis of miRNA sponge interaction networks and modules
Identification and analysis of miRNA sponge interaction networks and modules
Identification and analysis of miRNA sponge interaction networks and modules
Identify differentially expressed genes in microarray time-course data
Identifying Differential Effects in Tiling Microarray Data
Identifying differentially methylated regions efficiently with power and control
Identify likely duplicate samples from genomic or meta-data
Identify likely duplicate samples from genomic or meta-data
Identify likely duplicate samples from genomic or meta-data
Illumina 450K methylation array spatial analysis methods
Illumina 450 methylation array normalization and metrics
Illumina 450 methylation array normalization and metrics
Illumina methylation array analysis for large experiments
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
Improved Allele-Specific Copy Number of SNP Microarrays for Downstream Segmentation
impute: Imputation for microarray data
Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure
Inference of Chromosome-length Haplotypes using Genomic Data of Single Gamete Cells
Inference of Chromosome-Length Haplotypes Using Genomic Data of Single Gamete Cells
inference of invarsion alleles from biallelic haplotype clustering
Inference on agreement between ordered lists
Inference on agreement between ordered lists
Inferring miRNA sponge modules by integrating expression data and miRNA-target binding information
Inferring miRNA sponge modules by integrating expression data and miRNA-target binding information
Infers biological signatures from gene expression data
Integrated Analysis on two human genomic datasets
Integrated Analysis on two human genomic datasets
integrated Bayesian Modeling of eQTL data
integrated Bayesian Modeling of eQTL data
Integrating microRNA expression into signaling pathways for pathway analysis
Integration of Microarray Data for Meta-analysis
Integrative clustering of multi-type genomic data
Interactive HTML graphics
Interactive HTML graphics
Interactive visualization for Illumina methylation arrays
Interactive visualization for Illumina methylation arrays
Inversions in genotype data
ITALICS
JODA algorithm for quantifying gene deregulation using knowledge
KnowSeq R/Bioc package: Beyond the traditional Transcriptomic pipeline
KnowSeq R/Bioc package: Beyond the traditional Transcriptomic pipeline
L1-regularization based methods for detection of differential splicing
L1-regularization based methods for detection of differential splicing
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 Model Toolset for Gene Set Enrichment Analysis
LMGene Software for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays
Local Pooled Error Test for Differential Expression with Paired High-throughput Data
logit-t Package
LVS normalization for Agilent miRNA data
Mahalanobis Distance Quality Control for microarrays
Manipulation of Codelink microarray data
Manipulation of SQLite-based annotations in Bioconductor
Manipulation of SQLite-based annotations in Bioconductor
Manipulation of SQLite-based annotations in Bioconductor
Marker Gene Finder in Microarray gene expression data
masan uses bioconductor to analyze microarray data
Masking probes with binding affinity differences
massiR: MicroArray Sample Sex Identifier
massiR: MicroArray Sample Sex Identifier
massiR: MicroArray Sample Sex Identifier
massiR: MicroArray Sample Sex Identifier
Massive and Integrative Gene Set Analysis
Massive and Integrative Gene Set Analysis
Massive correlating biclusters for gene expression data and associated methods
Massive correlating biclusters for gene expression data and associated methods
Massive correlating biclusters for gene expression data and associated methods
Maximum Likelihood Estimation of DNA Methylation and Hydroxymethylation Proportions
Maximum Likelihood Estimation of DNA Methylation and Hydroxymethylation Proportions
MBCB (Model-based Background Correction for Beadarray)
Merge Maid
MetaAnalysis for High Throughput Experiments
MetaAnalysis for High Throughput Experiments
Methods for Affymetrix Oligonucleotide Arrays
Methods for analyzing microarray data using Local Pooled Error (LPE) method
Methods for fitting probe-level models
Methods for Spike-in Arrays
Methods for Spike-in Arrays
Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape
Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape
Methylated CpGs Set Enrichment Analysis
Methylated CpGs Set Enrichment Analysis
Methylation array and sequencing spatial analysis methods
Methylation array and sequencing spatial analysis methods
Methylation array and sequencing spatial analysis methods
MethyLiution: A QC Pipeline For Methylation Data
MiChip Parsing and Summarizing Functions
Microarray Analysis of Differential Expression
Microarray Analysis tool
MicroArray Chromosome Analysis Tool
MicroArray Gene-expression-based Program In Error rate estimation
Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Microrarray (AB1700) gene expression data.
Microarray Spot Segmentation and Gridding for Blocks of Microarray Spots
mimager: The Microarray Imager
mimager: The Microarray Imager
MiRNA Ranking by Gene Expression
miRNAtap: microRNA Targets - Aggregated Predictions
Misclassification Penalized Posterior Classification
Missing Value Estimation of DNA Methylation Data
MODA: MOdule Differential Analysis for weighted gene co-expression network
MODA: MOdule Differential Analysis for weighted gene co-expression network
Modeling Network State Transitions from Expression and Regulatory data (MONSTER)
Modeling Network State Transitions from Expression and Regulatory data (MONSTER)
Modelling Experimental Data from MeDIP Enrichment
Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their perturbation from controls
Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their perturbation from controls
Molecular Degree of Perturbation calculates scores for transcriptome data samples based on their perturbation from controls
Motif Identification and Validation
Motif Identification and Validation
Multiple Testing using SAM and Efron's Empirical Bayes Approaches
Multi sample aCGH analysis package using kernel convolution
Multivariate and directional gene set testing
Multivariate and directional gene set testing
Multivariate Correlation Estimator and Statistical Inference Procedures.
multivariate outlier detection for expression array QA
Murine Palate miRNA Expression Analysis
Muscle Epigenetic Age Test
Mutation Order Prediction
Mutual Information NETworks
Network reverse engineering from time course data.
Normalization of array CGH data with imbalanced aberrations.
Normal Uniform Differential Gene Expression detection
Nucleosome positioning package for R
Nucleosome positioning package for R
Nucleosome positioning package for R
Nucleosome positioning package for R
Objective Assessment of Copy-Number Estimates
Omics Data Integration Project
Omics Data Integration Project
Omics Data Integration Project
ontology enrichment analysis
Operating characteristics plus sample size and local fdr for microarray experiments
Optimized local intensity-dependent normalisation of two-color microarrays
Outlier detection using quantile regression on the M-A scatterplots of high-throughput data
Outlier Gene Set Analysis
Overlay omics data onto SBGN pathway diagram
Overlay omics data onto SBGN pathway diagram
Overlay omics data onto SBGN pathway diagram
PAA (Protein Array Analyzer)
Package for enabling powerful shiny web displays of Bioconductor objects
Package to work with miRNAs and miRNA targets with R
Pairwise INTegration of functional genomics data
Pairwise INTegration of functional genomics data
PANDA Algorithm
PANDA Algorithm
PANDA Algorithm
PANDA Algorithm
Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays
Parametric Gene Set Enrichment Analysis
Parsing Illumina Microarray Output Files
Parsing Illumina Microarray Output Files
PatchseqMap
PathoStat Statistical Microbiome Analysis Package
PathoStat Statistical Microbiome Analysis Package
Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)
PCA-based gene filtering for Affymetrix arrays
pcaGoPromoter is used to analyze DNA micro array data
Peptide Annotation and Data Visualization using Gviz
Peptide Annotation and Data Visualization using Gviz
Peptide microarray data package
Perform methylation analysis
Perform methylation analysis
Performs differential gene expression Analysis
Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA)
Permutation-Based Confidence for Molecular Classification
Phenotype prediction using microarray data: approach of the best overall team in the IMPROVER Diagnostic Signature Challenge
Pipeline for augmented co-expression analysis
Platform for integrative analysis of omics data
Platform for integrative analysis of omics data
Plots data (continuous/discrete) along chromosomal ideogram
Plots data (continuous/discrete) along chromosomal ideogram
Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
Plotting data and annotation information along genomic coordinates
Plotting data and annotation information along genomic coordinates
Plotting genomic information from Ensembl
Post-normalization of total copy numbers
Post-normalization of total copy numbers
Predict genes expressed selectively in specific cell types
Predict genes expressed selectively in specific cell types
Predicting Targets for Drosophila Intragenic miRNAs
Predicting Targets for Drosophila Intragenic miRNAs
Prepares microarray data for submission to GEO
Prepares microarray data for submission to GEO
Pre-process DNA Copy Number (CN) Data for Detection of CN Events
Preprocessing of Illumina Infinium 450K data
Preprocessing tools for oligonucleotide arrays
Preprocessing tools for oligonucleotide arrays
Preprocessing tools for oligonucleotide arrays
Preprocessing tools for oligonucleotide arrays.
Principal Coordinates and Hotelling's T-Square method
Principal Variance Component Analysis (PVCA)
Probabilistic combinatorial nested effects model
Probe Dependent Nearest Neighbours (PDNN) for the affy package
Probe-level Expression Change Averaging
Probe level Locally moderated Weighted t-tests.
Probe region expression estimation for RNA-seq data for improved microarray comparability
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 Orthogonal Space Testing for High Dimensional Data
Projection onto Orthogonal Space Testing for High Dimensional Data
PRojection Onto the Most Interesting Statistical Evidence
PROMISE analysis with Canonical Correlation for Two Forms of High Dimensional Genetic Data
PROMISE analysis with Canonical Correlation for Two Forms of High Dimensional Genetic Data
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 Report Generation for affyBatch objects
Qualitative biclustering algorithm for expression data analysis in R
Quality assessment and control for FFPE microarray expression data
Quality assessment and low-level analysis for Illumina BeadArray data
Quality assessment and low-level analysis for Illumina BeadArray data
Quality control for target capture experiments
Quality control for target capture experiments
Quality metrics and data processing methods for NanoString mRNA gene expression data
Quality metrics report for microarray data sets
Quality metrics report for microarray data sets
Quantify and interpret divers of variation in multilevel gene expression experiments
Quantify and interpret divers of variation in multilevel gene expression experiments
query gene expression data and plots from BrainStars (B*)
qusage: Quantitative Set Analysis for Gene Expression
qusage: Quantitative Set Analysis for Gene Expression
Random Rotation Methods for High Dimensional Data with Batch Structure
Random Rotation Methods for High Dimensional Data with Batch Structure
Rank Product method for identifying differentially expressed genes with application in meta-analysis
Rapid Reconstruction of Time-Varying Gene Regulatory Networks
RBioinf
RBM: a R package for microarray and RNA-Seq data analysis
RBM: a R package for microarray and RNA-Seq data analysis
Rcpp Integration Surrogate Variable Analysis
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
Regional Expression Biases
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
Removal of unwanted variation for gene-gene correlations and related analysis.
Repetitive Element Methylation Prediction
Repetitive Element Methylation Prediction
Reproducibility-Optimized Test Statistic
Reproducible GSEA Benchmarking
Reproducible GSEA Benchmarking
Resampling-based multiple hypothesis testing
Reversible Jump MCMC for the Analysis of CGH Arrays
R functions for the normalization of Exiqon miRNA array data
Rhythmicity Analysis Incorporating Non-parametric Methods
R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data.
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
R Investigation of ChIP-chip Oligoarrays
RNA-binding protein motif analysis
RNA-binding protein motif analysis
R Normalization and Inference of Time Series data
R Normalization and Inference of Time Series data
Robust Analysis of MicroArrays
Robust likelihood-based survival modeling with microarray data
R Onto-Tools suite
Routines for the functional analysis of biological networks
R package for calling CNV from Illumina 450k methylation microarrays
R package for combining multiple scans
RPA: Robust Probabilistic Averaging for probe-level analysis
RPA: Robust Probabilistic Averaging for probe-level analysis
runibic: row-based biclustering algorithm for analysis of gene expression data in R
Sample Classifier
Sample Classifier
Sample Size and Power Calculation in Micorarray Studies
Sample Size Calculation for RNA-Seq Experimental Design
Sample Size Calculation for RNA-Seq Experimental Design
Seamless navigation through combined results of set-based and network-based enrichment analysis
Seamless navigation through combined results of set-based and network-based enrichment analysis
Segmentation, normalisation and processing of aCGH data
Semi-supervised adaptive-height snipping of the Hierarchical Clustering tree
Semi-Supervised Mixture Model
Semi-Supervised Mixture Model
ShinyEPICO!
sigFeature: Significant feature selection using SVM-RFE & t-statistic
sigFeature: Significant feature selection using SVM-RFE & t-statistic
Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
Signal-to-Noise applied to Gene Expression Experiments
Significance of periodic expression pattern in time-series data
Significant Gene Expression Profile Differences in Time Course Gene Expression Data
Significant Gene Expression Profile Differences in Time Course Gene Expression Data
Similar Binding Profiles
Similarities of Ordered Gene Lists
Simple tiling array analysis of Affymetrix ChIP-chip data
simple Two-Tier Mapper: an interface for Two-Tier Mapper
Simplified RNA-Seq Analysis Pipeline
Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
Single-Sample Classifier of Medulloblastoma Subtypes for Medulloblastoma Patient Samples, Mouse Models, and Cell Lines
Single-Sample Classifier of Medulloblastoma Subtypes for Medulloblastoma Patient Samples, Mouse Models, and Cell Lines
Single-Sample Classifier of Medulloblastoma Subtypes for Medulloblastoma Patient Samples, Mouse Models, and Cell Lines
Smooth quantile normalization
Smooth quantile normalization
Smooth quantile normalization
SnpMatrix and XSnpMatrix classes and methods
SnpMatrix and XSnpMatrix classes and methods
Soft clustering of time series gene expression data
Sparse Contrastive Principal Component Analysis
Sparse Contrastive Principal Component Analysis
Spatial and intensity based normalization of cDNA microarray data based on robust neural nets
Sscore2: an R package for microarray analysis for Affymetrix/Thermo Fisher arrays
Statistical Analysis for Developmental Microarray Time Course Data
Statistical analysis of peptide microarrays
Statistical analysis of peptide microarrays
Statistical Analysis of the GeneChip
Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD)
Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD)
Statistics for Integrative Genomics Analyses in R
Stepwise Classification of Cancer Samples using High-dimensional Data Sets
Stepwise normalization functions for cDNA microarrays
Summarization and expression/phenotype association of CNV ranges
Summarization and expression/phenotype association of CNV ranges
SuperCurve RPPA Sample Data
Supervised Normalization of Microarrays
Supervised Normalization of Microarrays
Supporting Data Simulation R-package for quantro
Surrogate Variable Analysis
Surrogate Variable Analysis
Survival analysis for gene signatures
Synthetic Expression Data for Gene Regulatory Network Inference
Targeted Learning with Moderated Statistics for Biomarker Discovery
Targeted Learning with Moderated Statistics for Biomarker Discovery
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
Testing of SNPs and SNP Interactions in Case-Parent Trio Studies
The Bimodality Index
The Bimodality Index
The Discordant Method: A Novel Approach for Differential Correlation
The Discordant Method: A Novel Approach for Differential Correlation
The GASSCO method for correcting for slide-dependent gene-specific dye bias
The Genomic STate ANnotation Package
The Iterative Bayesian Model Averaging (BMA) algorithm
The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis
The removal of batch effects from datasets using a PCA and constrained optimisation based technique
The removal of batch effects from datasets using a PCA and constrained optimisation based technique
The 'snp.matrix' and 'X.snp.matrix' Classes
This package is designed to perform Gene Set Analysis across multiple genomic platforms
This package was built to cluster gene expression data using the Gaussian Infinite Mixture Model.
Time-Course Multi-Omics data integration
Time-Course Multi-Omics data integration
Time-Course Multi-Omics data integration
Tool for Evaluation of Cell Identity from Transcription Profiles
Tool for Evaluation of Cell Identity from Transcription Profiles
Tools for analyzing Micro Array experiments
Tools for Connectivity Map-like analyses
Tools for curating, analyzing, and manipulating biological sequences
Tools for Genome Wide Association Studies
Tools for Genome Wide Association Studies
Tools for Genome Wide Association Studies
Tools for HELP data analysis
Tools for making reports in various formats
Tools for making reports in various formats
Tools for manipulating GO and microarrays
Tools for manipulating GO and microarrays
Tools for microbiome analysis
Tools for parsing Affymetrix data files
Tools for the analysis of heterogeneous tissues
Tools for the analysis of heterogeneous tissues
Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level
Tools to test association between gene expression and phenotype in a way that is efficient, structured, fast and scalable. We also provide tools to do GSEA (Gene set enrichment analysis) and copy number variation.
Top Scoring Pairs for Microarray Classification
Transcriptional analysis based on transcriptograms
Transcriptional analysis based on transcriptograms
Transcriptional Regulatory Inference from Genetics of Gene ExpRession
Transcriptional Regulatory Inference from Genetics of Gene ExpRession
Transcription factor Inference through Gaussian process Reconstruction of Expression
Transcription factor Inference through Gaussian process Reconstruction of Expression
Transcript mapping with high-density oligonucleotide tiling arrays
Transcriptome instability analysis
Transcriptomic Ovarian Cancer Datasets
Transcriptomic Ovarian Cancer Datasets
Two-sample tests on a graph
Two-Tier Mapper: a clustering tool based on topological data analysis
Two-Tier Mapper: a clustering tool based on topological data analysis
Utilities to compute, compare, and plot the agreement between ordered vectors of features (ie. distinct genomic experiments). The package includes Correspondence-At-the-TOP (CAT) analysis.
Utilities to compute, compare, and plot the agreement between ordered vectors of features (ie. distinct genomic experiments). The package includes Correspondence-At-the-TOP (CAT) analysis.
Variance stabilization and calibration for microarray data
Variance stabilization in flow cytometry (and microarrays)
Very simple high level analysis of Affymetrix data
Visual and interactive gene expression analysis
Visual and interactive gene expression analysis
Visual and interactive gene expression analysis
Visual and interactive quality control of large Illumina DNA Methylation array data sets
Visual and interactive quality control of large Illumina DNA Methylation array data sets
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualize artificial correlation in microarray data
Visualize biclusters identified in gene expression data
Wavelet-Based Models for Tiling Array Transcriptome Analysis
waveTiling Example Data
XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression