Biocview "DifferentialExpression"

A bioconductor package for exploration of alignment gap positions from RNA-seq data
A bioconductor package for exploration of alignment gap positions from RNA-seq data
A bioconductor package for exploration of alignment gap positions from RNA-seq data
ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences
ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences
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
Active modules for multilayer weighted gene co-expression networks: a continuous optimization approach
Adaptive Gene Picking for Microarray Expression Data Analysis
Adaptive Gene Picking for Microarray Expression Data Analysis
Add-on to DESeq to improve p-values and q-values
Add-on to DESeq to improve p-values and q-values
Affected pathway ranking in differential gene expression analysis
Affymetrix Quality Assessment and Analysis Tool
Affymetrix Quality Assessment and Analysis Tool
A GAM based framework for analysis of ChIP-Seq data
A GAM based framework for analysis of ChIP-Seq data
A GAM based framework for analysis of ChIP-Seq data
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 user interface to conduct a dose-response analysis of microarray data
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
A Hybrid Feature Selection method for gene expression data
A Hybrid Feature Selection method for gene expression data
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
Analysis of alternative splicing using RNA-Seq
Analysis of alternative splicing using RNA-Seq
Analysis of alternative splicing using RNA-Seq
Analysis of alternative splicing using RNA-Seq
Analysis of amplicon enrichment panels
Analysis of amplicon enrichment panels
Analysis Of Differential Abundance Taking Sample Variation Into Account
Analysis Of Differential Abundance Taking Sample Variation Into Account
Analysis of Large Affymetrix Microarray Data Sets
Analysis of Large Affymetrix Microarray Data Sets
Analysis of Metabolomics GC/MS Data
Analysis of Metabolomics GC/MS Data
ANalysis Of Translational Activity (ANOTA).
ANalysis Of Translational Activity (ANOTA).
Analyze isomiRs and miRNAs from small RNA-seq
Analyze isomiRs and miRNAs from small RNA-seq
Analyze isomiRs and miRNAs from small RNA-seq
A new tool for exporting TCGA Firehose data
A new tool for exporting TCGA Firehose data
A new tool for exporting TCGA Firehose data
A new tool for exporting TCGA Firehose data
An integrated analysis package of Gene expression and Copy number alteration
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 integrated analysis package of miRNA and mRNA expression data
Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
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 retrieving data from DAVID into R objects using Web Services API.
An R Package for retrieving data from DAVID into R objects using Web Services API.
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 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 perform the network enrichment analysis (NEA).
A package for the clinical proteomic profiling data analysis
A package for the clinical proteomic profiling data analysis
A pile of (hopefully) useful R functions
Approximate posterior estimation for GLM coefficients
Artificial Components Detection of Differentially Expressed Genes
Artificial Components Detection of Differentially Expressed Genes
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 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 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).
Automated analysis of high-throughput qPCR data
Automated analysis of high-throughput qPCR data
A web interface for gene-set enrichment analyses
A web interface for gene-set enrichment analyses
Base Functions for Bioinformatics
Base Functions for Bioinformatics
Base Functions for Bioinformatics
Base Functions for Bioinformatics
Batch Effects Quality Control Software
Batch Effects Quality Control Software
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 Analysis of Differential Expression in RNA Sequencing Data
Bayesian Analysis of Differential Expression in RNA Sequencing Data
Bayesian Gene eXpression
Bayesian Gene eXpression
Bayesian models for differential gene expression
Bayesian models for differential gene expression
Bayesian Robust Inference for Differential Gene Expression
Bayesian Robust Inference for Differential Gene Expression
BIMEGA: BIvariate Methylation and Expression GAussian mixture model
Bioconductor Web Interface
Bioconductor Web Interface
BLMA: A package for bi-level meta-analysis
BLMA: A package for bi-level meta-analysis
BLMA: A package for bi-level meta-analysis
Calculates a global test for differential gene expression between groups
Calculates a global test for differential gene expression between groups
Calculates Mulcom test
Calculates Mulcom test
cancer outlier Gene Profile Sets
cancer outlier Gene Profile Sets
Causal network analysis methods
Causal network analysis methods
Characterization of Alternative Splicing based on Paired-End Reads
Characterization of Alternative Splicing based on Paired-End Reads
Classes and Methods for "Class Comparison" Problems on Microarrays
Classes and Methods for "Class Comparison" Problems on Microarrays
Classification of alternative splicing and prediction of coding potential from RNA-seq data.
Classification of alternative splicing and prediction of coding potential from RNA-seq data.
Classify diseases and build associated gene networks using gene expression profiles
Classify diseases and build associated gene networks using gene expression profiles
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
Clustering of Time Series Gene Expression data
Clustering of Time Series Gene Expression data
Clustering of Time Series Gene Expression 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
coexnet: An R package to build CO-EXpression NETworks from Microarray Data
Combination Connectivity Mapping
Combination Connectivity Mapping
Combination Connectivity Mapping
Comparison between multiple levels of gene expression
Comparison between multiple levels of gene expression
Comprehensive analysis of transciptome data
Comprehensive analysis of transciptome data
Computation of Gene Expression-Based Signatures in Breast Cancer
Computation of Gene Expression-Based Signatures in Breast Cancer
Computation of Gene Expression-Based Signatures in Breast Cancer
Compute coverage matrices from recount quickly using bwtool
ComSeq: An ensemble method for RNA-Seq differential analysis
ComSeq: An ensemble method for RNA-Seq differential analysis
Conditional quantile normalization
Conditional quantile normalization
Condition specific detection from expression data
Condition specific detection from expression data
Coordinated Gene Activity in Pattern Sets
Coordinated Gene Activity in Pattern Sets
Coordinated Gene Activity in Pattern Sets
Correlation Motif Fit
Correlation Motif Fit
Cross Platform Meta-Analysis of Microarray Data
Cross Platform Meta-Analysis of Microarray Data
Cross Platform Meta-Analysis of Microarray Data
csSAM - cell-specific Significance Analysis of Microarrays
debrowser: Interactive Differential Expresion Analysis Browser
debrowser: Interactive Differential Expresion Analysis Browser
debrowser: Interactive Differential Expresion Analysis Browser
Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data
Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data
Denoising Algorithm based on Relevance network Topology
Denoising Algorithm based on Relevance network Topology
derfinder helper package
derfinder helper package
derfinder helper package
DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments
DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments
DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments
Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM)
Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM)
DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates
DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates
Differential Enrichment analysis of Proteomics data
Differential expression analysis of longitudinal count data sets
Differential expression analysis of longitudinal count data sets
Differential expression analysis of longitudinal count data sets
Differential Expression Analysis of NanoString nCounter Data
Differential Expression Analysis of NanoString nCounter Data
Differential Expression via Distance Summary for Microarray Data
Differential Expression via Distance Summary for Microarray Data
Differential gene expression analysis based on the negative binomial distribution
Differential gene expression analysis based on the negative binomial distribution
Differential gene expression analysis based on the negative binomial distribution
Differential gene expression analysis based on the negative binomial distribution
Differential gene expression analysis based on the negative binomial distribution
Differential gene expression data formats converter
Differential gene expression data formats converter
Differential gene expression data formats converter
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
Dispersion shrinakge for sequencing data.
Dispersion shrinkage for sequencing data.
DNA IP-seq data analysis
DNA IP-seq data analysis
DNA IP-seq data analysis
DNA IP-seq data analysis
Dynamic Transcriptome Analysis
Dynamic Transcriptome Analysis
Earth Mover's Distance for Differential Analysis of Genomics Data
Earth Mover's Distance for Differential Analysis of Genomics Data
Earth Mover's Distance for Differential Analysis of Genomics Data
Easy Analysis of RNASeq DE
Easy Analysis of RNASeq DE
Efficient design and analysis of factorial two-colour microarray data
Efficient design and analysis of factorial two-colour microarray data
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
Engineering Evaluation by Gene Categorization (eegc)
Engineering Evaluation by Gene Categorization (eegc)
Engineering Evaluation by Gene Categorization (eegc)
Ensemble of Gene Set Enrichment Analyses
Ensemble of Gene Set Enrichment Analyses
Epigenetic and gene transcription data normalization and integration with mixture models
Epigenetic and gene transcription data normalization and integration with mixture models
Estimate Microarray Sample Size
Estimate Microarray Sample Size
Estimation of local false discovery rate
Estimation of local false discovery rate
Exon Based Strategy for Expression Analysis of genes
Exon Based Strategy for Expression Analysis of genes
Exploratory analysis and differential expression for RNA-seq data
Exploratory analysis and differential expression for RNA-seq data
Exploratory Data Analysis and Normalization for RNA-Seq
Exploratory Data Analysis and Normalization for RNA-Seq
Exploratory Data Analysis and Normalization for RNA-Seq
Explore and download data from the recount project
Explore and download data from the recount project
Explore and download data from the recount project
Exposome and omic data associatin and integration analysis
expression density diagnostics
Expression Weighted Celltype Enrichment
Expression Weighted Celltype Enrichment
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
Factorial designed microarray experiment analysis
Factorial designed microarray experiment analysis
Fast Gene Set Enrichment Analysis
Fast Gene Set Enrichment Analysis
Fast Gene Set Enrichment Analysis
Fast Permutation-based Gene Set Analysis
Fast Permutation-based Gene Set Analysis
Fast Permutation-based Gene Set Analysis
FDR adjustments of Microarray Experiments (FDR-AME)
FDR adjustments of Microarray Experiments (FDR-AME)
Filter replicated high-throughput transcriptome sequencing data
Filter replicated high-throughput transcriptome sequencing data
Flexible, isoform-level differential expression analysis
Flexible, isoform-level differential expression analysis
Flexible, isoform-level differential expression analysis
Flexible, isoform-level differential expression analysis
Functional Network Analysis
Functional Network Analysis
Functional Network Analysis
Functions to handle cDNA microarray data, including several methods of data analysis
Functions to handle cDNA microarray data, including several methods of data analysis
Functions to perform cancer outlier profile analysis.
Functions to perform cancer outlier profile analysis.
GaGa hierarchical model for high-throughput data analysis
GaGa hierarchical model for high-throughput data analysis
Gaussian Process Ranking and Estimation of Gene Expression time-series
Gaussian Process Ranking and Estimation of Gene Expression time-series
Gaussian Process Ranking and Estimation of Gene Expression time-series
geneChip Analysis Package
geneChip Analysis Package
Gene Expression Atlas query and gene set enrichment 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
Generally Applicable Gene-set Enrichment for Pathway Analysis
Generally Applicable Gene-set Enrichment for Pathway Analysis
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Gene Selection
Gene Selection
Gene selection based on the marginal distributions of gene profiles that characterized by a mixture of three-component multivariate distributions
Gene selection based on the marginal distributions of gene profiles that characterized by a mixture of three-component multivariate distributions
Gene Set Analysis in R
Gene Set Analysis in R
Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
Gene Set Enrichment / Projection Displays
Gene Set Enrichment / Projection Displays
Gene Set Regulation Index
Gene Set Regulation Index
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
Heterogeneous error model for identification of differentially expressed genes under multiple conditions
Heterogeneous error model for identification of differentially expressed genes under multiple conditions
Hierarchical Dependence in Meta-Analysis
Hierarchical Dependence in Meta-Analysis
High-Throughput Sequence Analysis using the Aroma Framework
Identification of Functional Epigenetic Modules
Identification of Functional Epigenetic Modules
Identification of genetic Variants affecting Alternative Splicing
Identification of genetic Variants affecting Alternative Splicing
Identify Differentially Expressed Genes from RNA-seq data
Identify Differentially Expressed Genes from RNA-seq data
Identify differentially expressed genes in microarray time-course data
Identify differentially expressed genes in microarray time-course data
Identifying Differential Effects in Tiling Microarray Data
Identifying Differential Effects in Tiling Microarray Data
Identify oncogenes and tumor suppressor genes from omics data
Identify oncogenes and tumor suppressor genes from omics data
Identify oncogenes and tumor suppressor genes from omics data
Illumina 450K methylation array spatial analysis methods
Inference of differential exon usage in RNA-Seq
Inference of differential exon usage in RNA-Seq
Integration of Microarray Data for Meta-analysis
Integration of Microarray Data for Meta-analysis
Integrative analysis of Multi-omics data for Alternative Splicing
Integrative analysis of Multi-omics data for Alternative Splicing
Integrative analysis of Multi-omics data for Alternative Splicing
Interactive Differential Expression AnaLysis
Interactive Differential Expression AnaLysis
Interactive HTML graphics
Interactive HTML graphics
Interactive HTML graphics
Interval-Wise Testing for Omics Data
Interval-Wise Testing for Omics Data
Interval-Wise Testing for Omics Data
Intron-Exon Retention Estimator
Intron-Exon Retention Estimator
Intron-Exon Retention Estimator
Isoform expression estimation based on RNA-seq data
JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data
JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data
L1-regularization based methods for detection of differential splicing
L1-regularization based methods for detection of differential splicing
L1-regularization based methods for detection of differential splicing
Laplace Mixture Model in Microarray Experiments
Laplace Mixture Model in Microarray Experiments
Linear model and normality based transformation method (Linnorm)
Linear model and normality based transformation method (Linnorm)
Linear Model decomposition for Designed Multivariate Experiments
Linear Model decomposition for Designed Multivariate Experiments
Linear Models for Microarray Data
Linear Models for Microarray Data
Linear Models for Microarray Data
LMGene Software for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays
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
Local Pooled Error Test for Differential Expression with Paired High-throughput Data
logit-t Package
logit-t Package
Long gene expression as a metric for neuronal identity
LPEseq: local-pooled-error test for RNA-seq data with a small number of replicates
LPEseq: local-pooled-error test for RNA-seq data with a small number of replicates
Merge Maid
Merge Maid
Meta-analysis of RNA-Seq count data in multiple studies
Meta-analysis of RNA-Seq count data in multiple studies
Meta-analysis of RNA-seq data
Meta-analysis of RNA-seq data
Methods for analyzing microarray data using Local Pooled Error (LPE) method
Methods for analyzing microarray data using Local Pooled Error (LPE) method
Methods for identifying small RNA loci from high-throughput sequencing data
Methods for identifying small RNA loci from high-throughput sequencing data
Methylation array and sequencing spatial analysis methods
Methylation array and sequencing spatial analysis methods
Methylation array and sequencing spatial analysis methods
MethylMix: Identifying methylation driven cancer genes
MethylMix: Identifying methylation driven cancer genes
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
Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
Microarray Analysis of Differential Expression
MicroArray Chromosome Analysis Tool
MicroArray Chromosome Analysis Tool
Microbial Assemblage Normalized Transcript Analysis
Microbial Assemblage Normalized Transcript Analysis
miRNApath: Pathway Enrichment for miRNA Expression Data
miRNApath: Pathway Enrichment for miRNA Expression Data
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
MODA: MOdule Differential Analysis for weighted gene co-expression network
MODA: MOdule Differential Analysis for weighted gene co-expression network
MODA: MOdule Differential Analysis for weighted gene co-expression network
Model-based Analysis of Single Cell Transcriptomics
Model-based Analysis of Single Cell Transcriptomics
Model-based Analysis of Single Cell Transcriptomics
Model-Based Gene Clustering for Genomics Data from Paired/Matched Designs
Multiple Beta t-Tests
Multiple Beta t-Tests
Multiple testing using SAM and Efron's empirical Bayes approaches
Multiple testing using SAM and Efron's empirical Bayes approaches
Multivariate and directional gene set testing
Multivariate and directional gene set testing
Murine Palate miRNA Expression Analysis
Murine Palate miRNA Expression Analysis
Normal Uniform Differential Gene Expression detection
Normal Uniform Differential Gene Expression detection
Obtain Raw Read Counts from RNASeq Data
Obtain Raw Read Counts from RNASeq Data
Operating characteristics plus sample size and local fdr for microarray experiments
Operating characteristics plus sample size and local fdr for microarray experiments
Package for Topology-based Pathway Analysis of RNASeq data
Package for Topology-based Pathway Analysis of RNASeq data
Pairwise Integration of Functional Genomics Data
Pairwise INTegration of functional genomics data
Pairwise INTegration of functional genomics data
Pathway Analysis
Pathway Analysis
Performance Assessment and Comparison for Survival Analysis
Performance Assessment and Comparison for Survival Analysis
Performance Assessment and Comparison for Survival Analysis
Performs differential gene expression Analysis
Performs differential gene expression Analysis
Permutation-Based Confidence for Molecular Classification
Permutation-Based Confidence for Molecular Classification
Platform for integrative analysis of omics data
Platform for integrative analysis of omics data
Plotting functions for derfinder
Plotting functions for derfinder
Plotting functions for derfinder
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 Coordinates and Hotelling's T-Square method
Probe-level Expression Change Averaging
Probe-level Expression Change Averaging
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
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)
PROspective Power Evaluation for RNAseq
PROspective Power Evaluation for RNAseq
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
Rank Product method for identifying differentially expressed genes with application in meta-analysis
Rank Product method for identifying differentially expressed genes with application in meta-analysis
R-based analysis of ChIP-seq And Differential Expression - a tool for integrating a count-based ChIP-seq analysis with differential expression summary data
R-based analysis of ChIP-seq And Differential Expression - a tool for integrating a count-based ChIP-seq analysis with differential expression summary data
RBM: a R package for microarray and RNA-Seq data analysis
RBM: a R package for microarray and RNA-Seq data analysis
Remove Unwanted Variation from RNA-Seq Data
Remove Unwanted Variation from RNA-Seq Data
Remove Unwanted Variation from RNA-Seq Data
Report of DEG analysis
Report of DEG analysis
Report of DEG analysis
Reproducibility-Optimized Test Statistic
Reproducibility-Optimized Test Statistic
Resampling-based multiple hypothesis testing
Resampling-based multiple hypothesis testing
Revealing differentially expressed genes using nonlinear dimensionality reduction for single cell RNA-Seq data
Revealing differentially expressed genes using nonlinear dimensionality reduction for single cell RNA-Seq data
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
R Interface with InterMine-Powered Databases
RNA-seq data analysis using the Poisson-Tweedie family of distributions
RNA-seq data analysis using the Poisson-Tweedie family of distributions
RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods
RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods
RnaSeqSampleSize
RnaSeqSampleSize
rnaSeq secondary analyses
rnaSeq secondary analyses
RNA-Seq Utilities
RNA-Seq Utilities
R Normalization and Inference of Time Series data
R Normalization and Inference of Time Series data
R Normalization and Inference of Time Series data
Routines for the functional analysis of biological networks
Routines for the functional analysis of biological networks
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
Sexual dimorphic and COPD differential analysis for gene expression and methylation.
signet: Selection Inference in Gene NETworks
Significance Analysis of Function and Expression
Significance Analysis of Function and Expression
Significance Analysis of Prognostic Signatures
Significance Analysis of Prognostic Signatures
Significance Analysis of Prognostic Signatures
Significance-based Modules Integrating the Transcriptome and Epigenome
Significance-based Modules Integrating the Transcriptome and Epigenome
Significance-based Modules Integrating the Transcriptome and Epigenome
Similarities of Ordered Gene Lists
Similarities of Ordered Gene Lists
Simplified RNA-Seq Analysis Pipeline
Simplified RNA-Seq Analysis Pipeline
Simulate RNA-seq reads
Simulate RNA-seq reads
Simulate RNA-seq reads
Simulate RNA-seq reads
Simulate RNA-seq reads
Single-Cell Consensus Clustering
Single-Cell Consensus Clustering
Single-Cell Consensus Clustering
Single Cell Differential Expression
Single Cell Differential Expression
Single Cell Differential Expression
Single-gene classifiers and outlier-resistant detection of differential expression for two-group and survival problems.
Single-gene classifiers and outlier-resistant detection of differential expression for two-group and survival problems.
small RNA-Seq Utilities
S-Score Algorithm for Affymetrix Oligonucleotide Microarrays
S-Score Algorithm for Affymetrix Oligonucleotide Microarrays
Stability and Aggregation of ranked gene lists
Stability and Aggregation of ranked gene lists
Statistical Analysis for Developmental Microarray Time Course Data
Statistical Analysis for Developmental Microarray Time Course Data
Statistical analysis for sparse high-throughput sequencing
Statistical analysis for sparse high-throughput sequencing
Statistical analysis for sparse high-throughput sequencing
Statistical analysis of sequins
Statistical analysis of sequins
Statistical analysis of sequins
Statistical Analysis of the GeneChip
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)
Statistical Tools for volume data from 2D Gel Electrophoresis
Statistical Tools for volume data from 2D Gel Electrophoresis
Statistics for Integrative Genomics Analyses in R
Statistics for Integrative Genomics Analyses in R
Subsampling of high-throughput sequencing count data
Subsampling of high-throughput sequencing count data
Subsampling of high-throughput sequencing count data
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
Supervised Normalization of Microarrays
Switch-like differential expression across single-cell trajectories
Switch-like differential expression across single-cell trajectories
Switch-like differential expression across single-cell trajectories
Targeted Learning for Biomarker Discovery with Moderated Statistics
Targeted Learning for Biomarker Discovery with Moderated Statistics
Targeted Learning for Biomarker Discovery with Moderated Statistics
TCC: Differential expression analysis for tag count data with robust normalization strategies
TCC: Differential expression analysis for tag count data with robust normalization strategies
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"
"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"
"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"
Test for differential expression for RNA-seq data
Test for differential expression for RNA-seq data
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 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
The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)
The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)
Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction
Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction
Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction
Time course sequencing data analysis
Time course sequencing data analysis
Time course sequencing data analysis
Tools for analyzing Micro Array experiments
Tools for analyzing Micro Array experiments
Tools for ordering single-cell sequencing
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.
Transcript expression inference and differential expression analysis for RNA-seq data
Transcript expression inference and differential expression analysis for RNA-seq data
Turn Bioconductor objects into tidy data frames
Turn Bioconductor objects into tidy data frames
Turn Bioconductor objects into tidy data frames
Two phase differential expression for singel-cell RNA-seq
Two-sample tests on a graph
Two-sample tests on a graph
Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification
Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification
Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data
Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data
utilities for ROC, with uarray focus
utilities for ROC, with uarray focus
Variance Adaptive Shrinkage
Very simple high level analysis of Affymetrix data
Very simple high level analysis of Affymetrix data
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
Wavelet-Based Models for Tiling Array Transcriptome Analysis
Wavelet-Based Models for Tiling Array Transcriptome Analysis
Wavelet-Based Models for Tiling Array Transcriptome Analysis
XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression
XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression