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 for the metagene package
A graphical interface for the metagene package
A lecture on sequence count data
Analysis of an ICA decomposition obtained on genomics data
Analysis of an ICA decomposition obtained on genomics data
Analytical R tools for Mass Spectrometry
Analytical R tools for Mass Spectrometry
Analytical R tools for Mass Spectrometry
An integrated analysis package of Gene expression and Copy number alteration
an R package for analysis, visualization and biomarker discovery of microbiome
an R package for analysis, visualization and biomarker discovery of microbiome
an R package for analysis, visualization and biomarker discovery of microbiome
an R package for analysis, visualization and biomarker discovery of microbiome
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 quantitative integration and analysis of multiple omics assays from heterogeneous samples
An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples
An R package for RNA visualization and analysis
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
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 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 to produce metagene plots
A package to produce metagene plots
A package to produce metagene plots
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 toolkit for performing KNN-based statistics for flow and mass cytometry data
A toolkit for performing KNN-based statistics for flow and mass cytometry data
a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.
a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.
Automated analysis of high-throughput qPCR data
BANDITS: Bayesian ANalysis of DIfferenTial Splicing
BANDITS: Bayesian ANalysis of DIfferenTial Splicing
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
Big multivariate data plotted interactively
Big multivariate data plotted interactively
Big multivariate data plotted interactively
Bump Hunter
Bump Hunter
Bump Hunter
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
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
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data
CommunityAMARETTO: A Computational Tool for the Discovery of Shared and Distinct Regulatory Mechanisms Across Biological Systems
Compare multiple ChIP-Seq experiments.
Condition specific detection from expression data
Controlling bias and inflation in association studies using the empirical null distribution
Coordinated Gene Activity in Pattern Sets
Coordinated Gene Activity in Pattern Sets
Covariate Assisted Large-scale Multiple testing
Covariate Assisted Large-scale Multiple testing
Data-Adaptive Statistics for High-Dimensional Multiple Testing
Data-Adaptive Statistics for High-Dimensional Multiple Testing
Decomposing Heterogeneous Cohorts using Omic Data Profiling
Decomposing Heterogeneous Cohorts using Omic Data Profiling
DESeq2 Analysis Utilities
DESeq2 Analysis Utilities
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing
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
dgeAnalysis
Differential Analyis of Hi-C Data
Differential Analysis 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
Disease Ontology Semantic and Enrichment analysis
Disease Ontology Semantic and Enrichment analysis
Disease Ontology Semantic and Enrichment analysis
Disease Ontology Semantic and Enrichment analysis
distinct: a method for differential analyses via hierarchical permutation tests
Empirical Analysis of Digital Gene Expression Data in R
Empirical Bayesian analysis of patterns of differential expression in count data
Empirical Method of Optimal Pvalue Weighting
Empirical RNA-seq Sample Size Analysis
Empirical RNA-seq Sample Size Analysis
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 the false discovery rate.
Evaluation of normalization methods and calculation of differential expression analysis statistics
Evaluation of normalization methods and calculation of differential expression analysis statistics
Exposome and omic data associatin and integration analysis
Exposome and omic data associatin and integration 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
FABIA: Factor Analysis for Bicluster Acquisition
FDR adjustments of Microarray Experiments (FDR-AME)
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
Fishpond: differential transcript and gene expression with inferential replicates
Fishpond: differential transcript and gene expression with inferential replicates
Functional Enrichment analysis
Functional Enrichment analysis
Functions to help analyze data as phyloseq objects
Functions to help analyze data as phyloseq objects
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
Generating Tree Hierarchy Visualizations from Gene Expression Data
Generating Tree Hierarchy Visualizations from Gene Expression Data
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
Global Test for Counts
Global Test for Counts
goProfiles: an R package for the statistical analysis of functional profiles
goProfiles: an R package for the statistical analysis of functional profiles
GPA (Genetic analysis incorporating Pleiotropy and Annotation)
GPA (Genetic analysis incorporating Pleiotropy and Annotation)
graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture
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 Two Color Microarrays
Handling and analysis of high-throughput microbiome census data
Handling and analysis of high-throughput microbiome census data
HLA typing clustering and visualization based on specific similarity metrics
HLA typing clustering and visualization based on specific similarity metrics
Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.
Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.
Identify Moonlighting ncRNAs
ID Mapping Analysis
ID Mapping Data Retrieval
ID Mapping Data Retrieval
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
Independent Hypothesis Weighting
Independent Hypothesis Weighting
Infers clonal composition of a tumor
In-silico methods for finemapping of genetic regions in inbred mice
In-silico methods for finemapping of genetic regions in inbred mice
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
Integrative Statistics of alleLe Dependent Expression
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
Linear Models for Microarray Data
LinkHD: a versatile framework to explore and integrate heterogeneous data
LinkHD: a versatile framework to explore and integrate heterogeneous data
LinkHD: a versatile framework to explore and integrate heterogeneous 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
Matched Interaction across Tissues (MIxT) data analysis
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
Metabarcoding and microbiome analysis using multiple amplicons
Methods for identifying small RNA loci from high-throughput sequencing data
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
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 identify genes with differential distributions
Mixture modeling of single-cell RNA-seq data to identify 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 Sequence Alignment
Multiple Testing using SAM and Efron's Empirical Bayes Approaches
Multiplex PCR Primer Design and Analysis
Multiplex PCR Primer Design and Analysis
Multivariate analysis of microarray data using ADE4
Murine Palate miRNA Expression Analysis
NGS Read Simulator for FFPE Tissue
NGS Read Simulator for FFPE Tissue
Normalization and difference calling in ChIP-seq data
Normalization and difference calling in ChIP-seq data
Omics Data Integration Project
Omics Data Integration Project
Omics Data Integration Project
Online error control
Online error control
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
OVESEG-test to detect tissue/cell-specific markers
OVESEG-test to detect tissue/cell-specific markers
Parametric And Resistant Outlier DYtection
Parametric And Resistant Outlier DYtection
Parametric And Resistant Outlier DYtection
Pathway Analysis
Permutation-Based Confidence for Molecular Classification
Phenotypic EMD for comparison of single-cell samples
Phenotypic EMD for comparison of single-cell samples
Phenotypic EMD for comparison of single-cell samples
PhyloProfile
PhyloProfile
PhyloProfile
Plot Gene Ontology and KEGG pathway Annotation and Abundance
Power Estimation Tool for RNA-Seq and proteomics data
Power Estimation Tool for RNA-Seq and proteomics data
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
Quantitative comparison of multiple ChIP-seq datasets
RBioinf
Rcpp Integration Surrogate Variable Analysis
Reactome Pathway Analysis
Reactome Pathway Analysis
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
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
Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries
Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries
Resampling-based multiple hypothesis testing
Resampling Collapsed Null Distributions for Simultaneous Inference
Resampling Collapsed Null Distributions for Simultaneous Inference
Resampling Collapsed Null Distributions for Simultaneous Inference
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
RNA-seq analysis using multiple algorithms
RNA-seq analysis using multiple algorithms
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
Semi-Supervised Mixture Model
Semi-Supervised Mixture Model
Set Based Visualizations for Next-Gen Sequencing Data
Set Based Visualizations for Next-Gen Sequencing Data
Shiny app GUI wrapper for ggplot with built-in statistical analysis
Shiny app GUI wrapper for ggplot with built-in statistical analysis
Significant Biology on a Gene Set
Similarities of Ordered Gene Lists
simple Two-Tier Mapper: an interface for Two-Tier Mapper
Single cell replicability analysis
Single cell replicability analysis
Smooth quantile normalization
Smooth quantile normalization
Smooth quantile normalization
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 of Molecular Profiles
Statistical Analysis of Molecular Profiles
Statistical Analysis of the GeneChip
Statistical Inference of Associations between Microbial Communities And host phenoTypes
Statistical Inference of Associations between Microbial Communities And host phenoTypes
Statistical Inference of Associations between Microbial Communities And host phenoTypes
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
Surrogate Variable Analysis
Surrogate Variable Analysis
Test and visualize gene overlaps
Testing multiple biological mediators simultaneously
Testing multiple biological mediators simultaneously
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
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 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.
Top Confident Effect Sizes
Top Confident Effect Sizes
trajectory-based differential expression analysis for sequencing data
trajectory-based differential expression analysis for sequencing data
Turn Bioconductor objects into tidy data frames
Turn Bioconductor objects into tidy data frames
TVTB: The VCF Tool Box
TVTB: The VCF Tool Box
Two-Tier Mapper: a clustering tool based on topological data analysis
Two-Tier Mapper: a clustering tool based on topological data analysis
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
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.
ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity
ViSEAGO: Easier data mining of biological functions organized into clusters using Gene Ontology and semantic similarity
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
Visualization of highly multiplexed imaging cytometry data in R
Visualization of highly multiplexed imaging cytometry data in R
Visualization of highly multiplexed imaging cytometry data in R