Biocview "MultipleComparison"

Adjust for positional and batch effects using ComBat
Adjust for positional and batch effects using ComBat
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
A graphical interface for the metagene package
A graphical interface for the metagene package
A graphical interface for the metagene package
Analysis of an ICA decomposition obtained on genomics data
Analysis of an ICA decomposition obtained on genomics data
An integrated analysis package of Gene expression and Copy number alteration
An integrated analysis package of Gene expression and Copy number alteration
An R package for gene and isoform differential expression analysis of RNA-seq data
An R package for gene and isoform differential expression analysis of RNA-seq data
An R package for gene and isoform differential expression analysis of RNA-seq data
An R package for pathway analysis using topological information
An R package for pathway analysis using topological information
An R package for qualitative biclustering in support of gene co-expression analyses
An R package for qualitative biclustering in support of gene co-expression analyses
An R package for RNA visualization and analysis
An R package for RNA visualization and analysis
An R package to detect chromatin state switches from epigenomic data
An R package to detect chromatin state switches from epigenomic data
An R package to detect chromatin state switches from epigenomic data
An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation
An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation
An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation
An R pipeline for .bed file annotation, comparing GO term enrichment between gene sets and data visualisation
A package for the clinical proteomic profiling data analysis
A package for the clinical proteomic profiling data analysis
A package to produce metagene plots
A package to produce metagene plots
A package to produce metagene plots
A small RNA-seq visualizer and analysis toolkit
A small RNA-seq visualizer and analysis toolkit
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
A test for when to use quantile normalization
A test for when to use quantile normalization
A test for when to use quantile normalization
Automated analysis of high-throughput qPCR data
Automated analysis of high-throughput qPCR data
Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments
Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments
Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments
Bayesian models for differential gene expression
Bayesian models for differential gene expression
Bump Hunter
Bump Hunter
Bump Hunter
Bump Hunter
Calculates Mulcom test
Calculates Mulcom test
ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
ChIP-Seq Analysis with Windows
ChIP-Seq Analysis with Windows
ChIP-Seq Analysis with Windows
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Clustering of high-throughput sequencing data by identifying co-expression patterns
Clustering of high-throughput sequencing data by identifying co-expression patterns
Clustering of high-throughput sequencing data by identifying co-expression patterns
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data
Compare multiple ChIP-Seq experiments.
Condition specific detection from expression data
Condition specific detection from expression data
Controlling bias and inflation in association studies using the empirical null distribution
Controlling bias and inflation in association studies using the empirical null distribution
Coordinated Gene Activity in Pattern Sets
Coordinated Gene Activity in Pattern Sets
Coordinated Gene Activity in Pattern Sets
Detecting SNPs with interactive effects on a quantitative trait
Detecting SNPs with interactive effects on a quantitative trait
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing
Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges
Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges
Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges
Differential Analyis of Hi-C Data
Differential Analyis of Hi-C Data
Differential Analyis of Hi-C Data
Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
DiffLogo: A comparative visualisation of biooligomer motifs
DiffLogo: A comparative visualisation of biooligomer motifs
DiffLogo: A comparative visualisation of biooligomer motifs
Disease Ontology Semantic and Enrichment analysis
Disease Ontology Semantic and Enrichment analysis
Disease Ontology Semantic and Enrichment analysis
Disease Ontology Semantic and Enrichment analysis
Empirical Analysis of Digital Gene Expression Data in R
Empirical Analysis of Digital Gene Expression Data in R
Empirical Bayesian analysis of patterns of differential expression in count data
Empirical Bayesian analysis of patterns of differential expression in count data
Empirical Method of Optimal Pvalue Weighting
Ensemble of Gene Set Enrichment Analyses
Ensemble of Gene Set Enrichment Analyses
Estimating Local False Discovery Rates Using Empirical Bayes Methods
Estimation of local false discovery rate
Estimation of local false discovery rate
Estimation of the false discovery rate.
Estimation of the false discovery rate.
Exposome and omic data associatin and integration analysis
Exposome exploration and outcome data analysis
Exposome exploration and outcome data analysis
Exposome exploration and outcome data analysis
Extraction of Differential Gene Expression
Extraction of Differential Gene Expression
Extraction of Differential Gene Expression
Extraction of Differential Gene Expression
FABIA: Factor Analysis for Bicluster Acquisition
FABIA: Factor Analysis for Bicluster Acquisition
FDR adjustments of Microarray Experiments (FDR-AME)
FDR adjustments of Microarray Experiments (FDR-AME)
Finding Co-occuring motifs of transcription factor binding sites
Finding Co-occuring motifs of transcription factor binding sites
Find the most characteristic gene ontology terms for groups of human genes
Find the most characteristic gene ontology terms for groups of human genes
Find the most characteristic gene ontology terms for groups of human genes
Find the most characteristic gene ontology terms for groups of human genes
GaGa hierarchical model for high-throughput data analysis
GaGa hierarchical model for high-throughput data analysis
Gene Environment Wide Interaction Search Threshold
Gene Environment Wide Interaction Search Threshold
Generally Applicable Gene-set Enrichment for Pathway Analysis
Generally Applicable Gene-set Enrichment for Pathway Analysis
Gene Set Analysis of (Rare) Copy Number Variants
Gene Set Analysis of (Rare) Copy Number Variants
Gene Set Analysis of (Rare) Copy Number Variants
Gene set over-representation, enrichment and network analyses for high-throughput screens
Gene set over-representation, enrichment and network analyses for high-throughput screens
goProfiles: an R package for the statistical analysis of functional profiles
goProfiles: an R package for the statistical analysis of functional profiles
goProfiles: an R package for the statistical analysis of functional profiles
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
GUI for limma package with Affymetrix microarrays
GUI for limma package with Affymetrix microarrays
GUI for limma package with two color microarrays
GUI for limma package with two color microarrays
Handling and analysis of high-throughput microbiome census data
Handling and analysis of high-throughput microbiome census data
Handling and analysis of high-throughput microbiome census data
ID Mapping Analysis
ID Mapping Analysis
ID Mapping Data Retrieval
ID Mapping Data Retrieval
ID Mapping Data Retrieval
Illumina 450K methylation array spatial analysis methods
Independent Hypothesis Weighting
Independent Hypothesis Weighting
Independent Hypothesis Weighting
Infers clonal composition of a tumor
Infers clonal composition of a tumor
Integrative analysis pipeline for pooled CRISPR functional genetic screens
Integrative Statistics of alleLe Dependent Expression
Integrative Statistics of alleLe Dependent Expression
Interactive Multi-Omics Cancers Data Visualization and Analysis
Interactive Multi-Omics Cancers Data Visualization and Analysis
Interactive Multi-Omics Cancers Data Visualization and Analysis
Interval-Wise Testing for Omics Data
Interval-Wise Testing for Omics Data
Interval-Wise Testing for Omics Data
Linear Models for Microarray Data
Linear Models for Microarray Data
Mapping cell populations in flow cytometry data for cross-sample comparisons using the Friedman-Rafsky Test
Mapping cell populations in flow cytometry data for cross-sample comparisons using the Friedman-Rafsky Test
Mapping cell populations in flow cytometry data for cross-sample comparisons using the Friedman-Rafsky Test
Matched Interaction across Tissues (MIxT) data analysis
MeSH Enrichment and Semantic analyses
MeSH Enrichment and Semantic analyses
MeSH Enrichment and Semantic analyses
Meta-analysis of high-throughput experiments using feature annotations
Meta-analysis of high-throughput experiments using feature annotations
Meta-analysis of high-throughput experiments using feature annotations
Meta-analysis of high-throughput experiments using feature annotations
Methods for identifying small RNA loci from high-throughput sequencing data
Methods for identifying small RNA loci from high-throughput sequencing data
Method to rapidly assess cell type identity using gene sets
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
Metrics to estimate a level of similarity between two ChIP-Seq profiles
Metrics to estimate a level of similarity between two ChIP-Seq profiles
Metrics to estimate a level of similarity between two ChIP-Seq profiles
Microarray Analysis of Differential Expression
Mixture modeling of single-cell RNA-seq data to indentify genes with differential distributions
Mixture modeling of single-cell RNA-seq data to indentify genes with differential distributions
Mixture modeling of single-cell RNA-seq data to indentify genes with differential distributions
Multiple Beta t-Tests
Multiple Beta t-Tests
Multiple co-inertia analysis of omics datasets
Multiple co-inertia analysis of omics datasets
Multiple co-inertia analysis of omics datasets
Multiple Sequence Alignment
Multiple Sequence Alignment
Multiple testing using SAM and Efron's empirical Bayes approaches
Multiple testing using SAM and Efron's empirical Bayes approaches
Multivariate analysis of microarray data using ADE4
Multivariate analysis of microarray data using ADE4
Murine Palate miRNA Expression Analysis
Murine Palate miRNA Expression Analysis
Normalization and difference calling in ChIP-seq data
Normalization and difference calling in ChIP-seq data
Normalization and difference calling in ChIP-seq data
Operating characteristics plus sample size and local fdr for microarray experiments
Operating characteristics plus sample size and local fdr for microarray experiments
Optimal p-value weighting with independent information
Optimal p-value weighting with independent information
Optimal p-value weighting with independent information
Parametric And Resistant Outlier DYtection
Parametric And Resistant Outlier DYtection
Pathway Analysis
Pathway Analysis
Permutation-Based Confidence for Molecular Classification
Permutation-Based Confidence for Molecular Classification
Prize: an R package for prioritization estimation based on analytic hierarchy process
Prize: an R package for prioritization estimation based on analytic hierarchy process
Produce heatmaps for RNA-Seq HIV data
PRojection Onto the Most Interesting Statistical Evidence
PRojection Onto the Most Interesting Statistical Evidence
Quantitative comparison of multiple ChIP-seq datasets
Quantitative comparison of multiple ChIP-seq datasets
RBioinf
RBioinf
Rcpp Integration Surrogate Variable Analysis
Reactome Pathway Analysis
Reactome Pathway Analysis
Reactome Pathway Analysis
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
Resampling-based multiple hypothesis testing
Resampling-based multiple hypothesis testing
Rhythmicity Analysis Incorporating Non-parametric Methods
Rhythmicity Analysis Incorporating Non-parametric Methods
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
Run metabarcoding alalyses for multiple amplicons
Science-wise false discovery rate and proportion of true null hypotheses estimation
Science-wise false discovery rate and proportion of true null hypotheses estimation
Science-wise false discovery rate and proportion of true null hypotheses estimation
Science-wise false discovery rate and proportion of true null hypotheses estimation
Similarities of Ordered Gene Lists
Similarities of Ordered Gene Lists
Smooth quantile normalization
Smooth quantile normalization
Stability Ranking
Stability Ranking
statistical analysis and visualization of functional profiles for genes and gene clusters
statistical analysis and visualization of functional profiles for genes and gene clusters
statistical analysis and visualization of functional profiles for genes and gene clusters
statistical analysis and visualization of functional profiles for genes and gene clusters
Statistical analysis for sparse high-throughput sequencing
Statistical analysis for sparse high-throughput sequencing
Statistical analysis for sparse high-throughput sequencing
Statistical Analysis of the GeneChip
Statistical Analysis of the GeneChip
Statistical Testing for ChIP-Seq data sets
Statistical Tools for volume data from 2D Gel Electrophoresis
Statistical Tools for volume data from 2D Gel Electrophoresis
Statistics and dIagnostic Graphs for HTS
Statistics and dIagnostic Graphs for HTS
Suite of Functions for Pooled Crispr Screen QC and Analysis
Suite of Functions for Pooled Crispr Screen QC and Analysis
Suite of Functions for Pooled Crispr Screen QC and Analysis
Supervised Normalization of Microarrays
Supervised Normalization of Microarrays
Surrogate Variable Analysis
Surrogate Variable Analysis
Surrogate Variable Analysis
Test and visualize gene overlaps
Test and visualize gene overlaps
Testing for association between RNA-Seq and high-dimensional data
Testing for association between RNA-Seq and high-dimensional data
Testing for association between RNA-Seq and high-dimensional data
Testing multiple biological mediators simultaneously
Testing multiple biological mediators simultaneously
Testing multiple biological mediators simultaneously
The double Kolmogorov-Smirnov package for evaluating multiple testing procedures.
The double Kolmogorov-Smirnov package for evaluating multiple testing procedures.
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 removal of batch effects from datasets using a PCA and constrained optimisation based technique
Tools for manipulating GO and microarrays
Tools for manipulating GO and microarrays
Tools for manipulating GO and microarrays
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.
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.
Turn Bioconductor objects into tidy data frames
Turn Bioconductor objects into tidy data frames
Turn Bioconductor objects into tidy data frames
TVTB: The VCF Tool Box
TVTB: The VCF Tool Box
TVTB: The VCF Tool Box
TVTB: The VCF Tool Box
Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data
Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data
Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data
Using Mass Cytometry for Differential Abundance Analyses
Using Mass Cytometry for Differential Abundance Analyses
Using Mass Cytometry for Differential Abundance Analyses
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.
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
Visualise microarray and RNAseq data using gene ontology annotations