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
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
A Comprehensive R Package For Analyzing Quantitative Phosphoproteomics Data
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
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
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 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
A Minimum Enclosing Ball (MEB) method to detect differential expression genes for RNA-seq 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 for short time-series data
Analysis for short time-series data
Analysis for short time-series data
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 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 Time-Resolved RNA-Seq Data
Analysis of Time-Resolved RNA-Seq Data
ANalysis Of Translational Activity (ANOTA).
Analysis routines over a FacileDataStore
Analysis routines over a FacileDataStore
Analytical R tools for Mass Spectrometry
Analytical R tools for Mass Spectrometry
Analytical R tools for Mass Spectrometry
Analyze isomiRs and miRNAs from small RNA-seq
Analyze isomiRs and miRNAs from small RNA-seq
Analyze small RNA-seq count 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 Implementation of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection
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
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
A normalization-invariant minimum enclosing ball method to detect differentially expressed genes for 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 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 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 for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.
A package for the clinical proteomic profiling data analysis
A package of creating an algorithm of identifying microRNA-competing endogenous RNA triplets
A Package to Download, Organize and Analyze Genomic Data Commons (GDC) Data
A pile of (hopefully) useful R functions
Approximate posterior estimation for GLM coefficients
Approximate posterior estimation for GLM coefficients
A Rank Based Approach to Modeling Gene Expression
A Rank Based Approach to Modeling Gene Expression
Artificial Components Detection of Differentially Expressed Genes
ascend - Analysis of Single Cell Expression, Normalisation, and Differential expression
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 statistical normalization method and differential expression analysis for RNA-seq data between different species
A statistical normalization method and differential expression analysis for RNA-seq data between different species
A tool for differential expression analysis and DEGs based investigation to complex diseases by bi-clustering analysis
A tool for differential expression analysis and DEGs based investigation to complex diseases by bi-clustering analysis
A tool for differential expression analysis and DEGs based investigation to complex diseases by bi-clustering analysis
A toolkit for APA analysis using RNA-seq data
A toolkit for APA analysis using RNA-seq 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 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.
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 unified computational framework for genomic feature annotation, differential expression analysis of circular RNAs
A unified interface to a plethora of gene set enrichment analysis methods
A user friendly R package to perform the network enrichment analysis (NEA).
Automated analysis of high-throughput qPCR data
A visualization tool for single cell data of C.elegans embrogenesis
A web interface for gene-set enrichment analyses
BANDITS: Bayesian ANalysis of DIfferenTial Splicing
BANDITS: Bayesian ANalysis of DIfferenTial Splicing
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 of Differential Expression in RNA Sequencing Data
Bayesian Analysis of Single-Cell Sequencing data
Bayesian Analysis of Single-Cell Sequencing data
Bayesian Gene eXpression
Bayesian models for differential gene expression
Bayesian Robust Inference for Differential Gene Expression
bcbio RNA-Seq
bcbio RNA-Seq
Bias Awared Peak Calling and Quantification for MeRIP-Seq
Bias Awared Peak Calling and Quantification for MeRIP-Seq
Bias Awared Peak Calling and Quantification for MeRIP-Seq
Big multivariate data plotted interactively
Big multivariate data plotted interactively
Big multivariate data plotted interactively
BIMEGA: BIvariate Methylation and Expression GAussian mixture model
Bioc2019PanCancerStudy
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
cancer outlier Gene Profile Sets
Category encoding method for selecting feature genes for the classification of single-cell RNA-seq
Category encoding method for selecting feature genes for the classification of single-cell RNA-seq
Causal network analysis methods
Characterization of Alternative Splicing based on Paired-End Reads
circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs
circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs
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.
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 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
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
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
CommunityAMARETTO: A Computational Tool for the Discovery of Shared and Distinct Regulatory Mechanisms Across Biological Systems
Comparing Differential Abundance/Expression Methods
Comparison between multiple levels of gene expression
Comprehensive analysis of transciptome data
Comprehensive analysis of transcriptome data
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
Condition specific detection from expression data
Coordinated Gene Activity in Pattern Sets
Coordinated Gene Activity in Pattern Sets
Correlation Motif Fit
Covariate Assisted Large-scale Multiple testing
Covariate Assisted Large-scale Multiple testing
Create rapid visualizations of RNAseq data in R
Create rapid visualizations of RNAseq data in R
Create rapid visualizations of RNAseq data in R
Create rapid visualizations of RNAseq data in R
Creation and Analysis of Pathway Expression Profiles (PEPs)
Creation and Analysis of Pathway Expression Profiles (PEPs)
Cross Platform Meta-Analysis of Microarray Data
Cross Platform Meta-Analysis of Microarray Data
csSAM - cell-specific Significance Analysis of Microarrays
Cytometry dATa anALYSis Tools
Cytometry dATa anALYSis Tools
Data-Adaptive Statistics for High-Dimensional Multiple Testing
Data-Adaptive Statistics for High-Dimensional Multiple Testing
Data package for query/retrieval of species specific MSigDB versions
Data package for query/retrieval of species specific MSigDB versions
Decomposing Heterogeneous Cohorts using Omic Data Profiling
Decomposing Heterogeneous Cohorts using Omic Data Profiling
Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data
DegNorm: degradation normalization for RNA-seq data
Delineate outstanding genomic zones of differential gene activity
Delineate outstanding genomic zones of differential gene activity
Denoising Algorithm based on Relevance network Topology
derfinder helper package
derfinder helper package
DESeq2 Analysis Utilities
DESeq2 Analysis Utilities
DEsingle for detecting three types of differential expression in single-cell RNA-seq data
DEsingle for detecting three types of differential expression in single-cell RNA-seq data
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)
Detecting Differentially Variable Genes Using the Mixture of Marginal Distributions
Detecting Gene Probes with Different Means or Variances Between Two Groups
Determination of essential phenotypic elements of clusters in high-dimensional entities
Determination of essential phenotypic elements of clusters in high-dimensional entities
DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates
dgeAnalysis
Differential Abundance Analysis of Label-Free Mass Spectrometry Data
Differential Abundance Analysis of Label-Free Mass Spectrometry Data
Differential Abundant Analysis for Metabolomics and Proteomics Data
Differential Abundant Analysis for Metabolomics and Proteomics Data
Differential Co-expression Analysis
Differential Co-expression Analysis
Differential co-expression/association network analysis
Differential Enrichment analysis of Proteomics data
Differential Enrichment analysis of Proteomics data
Differential Enrichment analysis of Proteomics data
Differential Epigenetic Coregulation Test
Differential Expressed Windows Based on Negative Binomial Distribution
Differential expression analysis and model fitting for single-cell RNA-seq data
Differential expression analysis and model fitting for single-cell RNA-seq data
Differential Expression Analysis for RNA-seq data through a robust variance component test
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 Analysis of NanoString nCounter 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 usage in immune repertoires
Differential gene usage in immune repertoires
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 shrinkage for sequencing data
Dispersion shrinkage for sequencing data
distinct: a method for differential analyses via hierarchical permutation tests
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
doseLM
doseR
doseR
doseR
doseR
doseR
Dynamic Transcriptome Analysis
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
Empirical Analysis of Digital Gene Expression Data in R
Empirical Bayesian analysis of patterns of differential expression in count data
Empirical RNA-seq Sample Size Analysis
Empirical RNA-seq Sample Size Analysis
Engineering Evaluation by Gene Categorization (eegc)
Engineering Evaluation by Gene Categorization (eegc)
Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis
Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis
Ensemble of Gene Set Enrichment Analyses
Ensemble of Gene Set Enrichment Analyses
Environment for Gene Expression Searching Combined with Functional Enrichment Analysis
Environment for Gene Expression Searching Combined with Functional Enrichment Analysis
Epigenetic and gene transcription data normalization and integration with mixture models
Estimate Microarray Sample Size
Estimation of local 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
Example experimental microarray data set for the "biotmle" R package
Exon Based Strategy for Expression Analysis of genes
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
Explore and download data from the recount3 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
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
FABIA: Factor Analysis for Bicluster Acquisition
Factorial designed microarray experiment analysis
Fast Gene Set Enrichment Analysis
Fast Gene Set Enrichment Analysis
Fast Permutation-based Gene Set Analysis
Fast Permutation-based Gene Set Analysis
FDR adjustments of Microarray Experiments (FDR-AME)
Filter replicated high-throughput transcriptome sequencing data
Filter replicated high-throughput transcriptome sequencing data
Finding an Active Metabolic Module in Atom Transition Network
Finding differentially expressed unannotated genomic regions from RNA-seq data
Finding differentially expressed unannotated genomic regions from RNA-seq data
Fishpond: differential transcript and gene expression with inferential replicates
Fishpond: differential transcript and gene expression with inferential replicates
Flexible, isoform-level differential expression analysis
Flexible, isoform-level differential expression analysis
Flexible, isoform-level differential expression analysis
For Visualizing Differential Expression Analysis
Functional Network Analysis
Functional Network Analysis
Functions to handle cDNA microarray data, including several methods of data analysis
Functions to perform cancer outlier profile 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
GCSscore: an R package for microarray analysis for Affymetrix/Thermo Fisher arrays
GCSscore: an R package for microarray analysis for Affymetrix/Thermo Fisher arrays
GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC
GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC
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 Meta-analysis Visualization Tool
Gene Expression Meta-analysis Visualization Tool
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
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
Generating Tree Hierarchy Visualizations from Gene Expression Data
Generating Tree Hierarchy Visualizations from Gene Expression Data
Gene regulator enrichment analysis
Gene Selection
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 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 Analysis with Networks
Gene Set Enrichment Analysis with Networks
Gene Set Enrichment / Projection Displays
Gene Set Enrichment / Projection Displays
Gene Set Regulation Index
Genotype Imputed Gene Set Enrichment Analysis
Genotype Imputed Gene Set Enrichment Analysis
Global Test for Counts
Global Test for Counts
Global test for groups of variables via model comparisons
Global test for groups of variables via model comparisons
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 Exploration of Design Matrices
Graphical Exploration of Design Matrices
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
Heterogeneity-Induced Pre-Processing tOol
Heterogeneity-Induced Pre-Processing tOol
Heterogeneous error model for identification of differentially expressed genes under multiple conditions
Hierarchical Dependence in Meta-Analysis
High-Throughput Sequence Analysis using the Aroma Framework
Identification of candidate causal perturbations from differential gene expression data
Identification of candidate causal perturbations from differential gene expression data
Identification of CTC in Blood Streams
Identification of Functional Epigenetic Modules
Identification of genetic Variants affecting Alternative Splicing
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 Differentially Expressed Genes from RNA-seq data
Identify differentially expressed genes in microarray time-course 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
Illumina 450K methylation array spatial analysis methods
ILoReg enables high-precision cell population identification from scRNA-Seq data
ImagingAMARETTO: tools for interpreting multi-omics networks for relevance to clinical outcomes and radiographic and histopathology imaging-derived biomarkers
Inference of differential exon usage in RNA-Seq
Inference of differential exon usage in RNA-Seq
Inferring unobserved perturbations from gene expression data
Integrated Differential Expression and Differential Network Analysis (INDEED)
Integrating Cap Enrichment with Transcript Expression Analysis
Integrating Cap Enrichment with Transcript Expression 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
Interactive Analysis of Single Cell RNA-Seq Data
Interactive Analysis of Single Cell RNA-Seq Data
Interactive Analysis of Single Cell RNA-Seq Data
Interactive Differential Expresion Analysis Browser
Interactive Differential Expresion Analysis Browser
Interactive Differential Expresion Analysis Browser
Interactive Differential Expression AnaLysis
Interactive Differential Expression AnaLysis
Interactive Differential Expression AnaLysis
Interactive HTML graphics
Interactive HTML graphics
Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package
Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package
Interval-Wise Testing for Omics Data
Interval-Wise Testing for Omics Data
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
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
Linear model and normality based normalization and transformation method (Linnorm)
Linear Model decomposition for Designed Multivariate Experiments
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
Local Pooled Error Test for Differential Expression with Paired High-throughput Data
Log fold change distribution tools for working with ratios of counts
Log fold change distribution tools for working with ratios of counts
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
Maximum Likelihood Decay Modeling of RNA Degradation Data
Maximum Likelihood Decay Modeling of RNA Degradation Data
Merge Maid
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 identifying small RNA loci from high-throughput sequencing data
Methylation Analysis Based on Signal Detection
Methylation array and sequencing spatial analysis methods
Methylation array and sequencing spatial analysis methods
Methylation array and sequencing spatial analysis methods
MethylIT utility
MethylMix: Identifying methylation driven cancer genes
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
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
Microbial Assemblage Normalized Transcript Analysis
Microbial Assemblage Normalized Transcript Analysis
Minimized Single-Cell Consensus Clustering
Minimized Single-Cell Consensus Clustering
miRNApath: Pathway Enrichment for miRNA Expression Data
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
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 Gene Clustering for Genomics Data from Paired/Matched Designs
Multi-Contrast Gene Set Enrichment Analysis
Multi-Contrast Gene Set Enrichment Analysis
Multi-Contrast Gene Set Enrichment Analysis
Multi-Dataset Model-based Differential Expression Proteomics Analysis Platform
Multi-Dataset Model-based Differential Expression Proteomics Analysis Platform
Multi matrix analysis of multiple proteomics datasets on peptide level
Multiple Beta t-Tests
Multiple Beta t-Tests
Multiple Testing using SAM and Efron's Empirical Bayes Approaches
Multi-sample multi-group scRNA-seq data analysis tools
Multi-sample multi-group scRNA-seq data analysis tools
Multi-sample multi-group scRNA-seq data analysis tools
Multivariate and directional gene set testing
Multivariate and directional gene set testing
Murine Palate miRNA Expression Analysis
NanoString data normalization and differential gene expression analysis
Negative Binomial Additive Model for RNA-Seq Data
Negative Binomial Additive Model for RNA-Seq Data
Negative Binomial Models to detect Differential Splicing
Negative Binomial Models to detect Differential Splicing
Network Perturbation Amplitude
Network Perturbation Amplitude
NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment
NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment
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
Outlier Analysis for pairwise differential comparison
Outlier Analysis for pairwise differential comparison
Outlier Analysis for pairwise differential comparison
Outlier Protein and Phosphosite Target Identifier
Outlier Protein and Phosphosite Target Identifier
Overlay omics data onto SBGN pathway diagram
Overlay omics data onto SBGN pathway diagram
Overlay omics data onto SBGN pathway diagram
Package for Fold-specific GO Terms Recognition
Package for Fold-specific GO Terms Recognition
Package for Fold-specific GO Terms Recognition
PAIRADISE: Paired analysis of differential isoform expression
PAIRADISE: Paired analysis of differential isoform expression
Pairwise INTegration of functional genomics data
Pairwise INTegration of functional genomics data
PatchseqMap
Pathway Analysis
PEBBA
Performance Assessment and Comparison for Survival Analysis
Performance Assessment and Comparison for Survival Analysis
Performs differential gene expression Analysis
Permutation-Based Confidence for Molecular Classification
pinnacle: Gene set enrichment analysis based on genomic intervals
Pipelines for Bi-Clustering Using Matrix Factorization
Platform for integrative analysis of omics data
Platform for integrative analysis of omics data
Plotting functions for derfinder
Plotting functions for derfinder
Point Resizing for Volcano Plots
PoTRA: Pathways of Topological Rank Analysis
PoTRA: Pathways of Topological Rank Analysis
PoTRA: Pathways of Topological Rank Analysis
Power Estimation Tool for RNA-Seq and proteomics data
Power Estimation Tool for RNA-Seq and proteomics 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
Probe-level Expression Change Averaging
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 Differential Expression Analysis of Agilent microRNA chips
Profile RA-Seq Data Using TB Pathway Signatures
Profile RA-Seq Data Using TB Pathway Signatures
Profile RA-Seq Data Using TB Pathway Signatures
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
Provides shiny components to visualize multilGSEA results
Publication-ready volcano plots with enhanced colouring and labeling
Publication-ready volcano plots with enhanced colouring and labeling
Putting the fun in LINCS L1000 data analysis
Putting the fun in LINCS L1000 data analysis
Putting the fun in LINCS L1000 data analysis
QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data
Quantification and Visulization of Variations of Splicing in Population
Quantification and Visulization of Variations of Splicing in Population
Quantification and Visulization of Variations of Splicing in Population
Quantification and Visulization of Variations of Splicing in Population
Quantify and interpret divers of variation in multilevel gene expression experiments
Quantify and interpret divers of variation in multilevel gene expression experiments
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
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
Reconstruction, visualization and analysis of branching trajectories
Reconstruction, visualization and analysis of branching trajectories
Reconstruction, visualization and analysis of branching trajectories
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
Remove Unwanted Variation from RNA-Seq Data
Remove Unwanted Variation from RNA-Seq Data
Report of DEG analysis
Report of DEG analysis
Reproducibility-Optimized Test Statistic
Reproducible GSEA Benchmarking
Reproducible GSEA Benchmarking
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
R Interface with InterMine-Powered Databases
RNA-binding protein motif analysis
RNA-binding protein motif analysis
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
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
RnaSeqSampleSize
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
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
Signature-based Clustering for Diagnostic Purposes
Signature-based Clustering for Diagnostic Purposes
Signature-based Clustering for Diagnostic Purposes
signet: Selection Inference in Gene NETworks
signet: Selection Inference in Gene NETworks
Significance Analysis of Function and Expression
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
simple Two-Tier Mapper: an interface for Two-Tier Mapper
Simplified RNA-Seq Analysis Pipeline
Simulate RNA-seq reads
Simulate RNA-seq reads
Simulate RNA-seq reads
Simulate RNA-seq reads
Simulation tool for optimal design of high-dimensional MS-based proteomics experiment
Simulation tool for optimal design of high-dimensional MS-based proteomics experiment
Single-Cell Consensus Clustering
Single-Cell Consensus Clustering
Single Cell Differential Expression
Single Cell Differential Expression
Single-gene classifiers and outlier-resistant detection of differential expression for two-group and survival problems
small RNA-Seq Utilities
Sparse Contrastive Principal Component Analysis
Sparse Contrastive Principal Component Analysis
Sscore2: an R package for microarray analysis for Affymetrix/Thermo Fisher arrays
S-Score Algorithm for Affymetrix Oligonucleotide Microarrays
Stability and Aggregation of ranked gene lists
Statistical Analysis for Developmental Microarray Time Course Data
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 MPRA data
Statistical Analysis of MPRA data
Statistical analysis of sequins
Statistical analysis of sequins
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 Inferences with MeDIP-seq Data (SIMD) to infer the methylation level for each CpG site
Statistical Inferences with MeDIP-seq Data (SIMD) to infer the methylation level for each CpG site
Statistical tests for detecting differential distributions based on the 2-Wasserstein distance
Statistical tests for detecting differential distributions based on the 2-Wasserstein distance
Statistical tests for detecting differential distributions based on the 2-Wasserstein distance
Statistical Tools for volume data from 2D Gel Electrophoresis
Statistics for Integrative Genomics Analyses in R
Stoichiometry analysis of label-free proteomics data
Subsampling of high-throughput sequencing count data
Subsampling of high-throughput sequencing count data
Suffix Array Kernel Smoothing for discovery of correlative sequence motifs and multi-motif domains
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
Summarization and expression/phenotype association of CNV ranges
Summarization and expression/phenotype association of CNV ranges
Supervised Normalization of Microarrays
Supervised Normalization of Microarrays
Switch-like differential expression across single-cell trajectories
Switch-like differential expression across single-cell trajectories
Targeted Learning with Moderated Statistics for Biomarker Discovery
Targeted Learning with Moderated Statistics for Biomarker Discovery
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
"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
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)
this package collects r fxns useful in my daily coding life
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
Tools for analyzing Micro Array experiments
Tools for ordering single-cell sequencing
Tools for ordering single-cell sequencing
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 Confident Effect Sizes
Top Confident Effect Sizes
Topology-based pathway analysis of RNA-seq data
Topology-based pathway analysis of RNA-seq data
trajectory-based differential expression analysis for sequencing data
trajectory-based differential expression analysis for sequencing data
Transcript expression inference and differential expression analysis for RNA-seq data
Transcriptional analysis based on transcriptograms
Transcriptional analysis based on transcriptograms
Transform Counts in RNA-Seq Data Analysis
Translational control assessment from ribosome footprint and total RNA libraries
Tumor subclonality of expression-based cancer subtypes
Turn Bioconductor objects into tidy data frames
Turn Bioconductor objects into tidy data frames
Two phase differential expression for singel-cell RNA-seq
Two phase differential expression for single-cell RNA-seq
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
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 microarray focus
Variance Adaptive Shrinkage
Very simple high level analysis of Affymetrix data
Viscello for Visualization of Single Cell Data
Viscello for Visualization of Single Cell Data
Viscello for Visualization of Single Cell EHT Data
Visual and interactive gene expression analysis
Visual and interactive gene expression analysis
Visual and interactive gene expression analysis
Visual Exploration of Omic Datasets Using a Shiny App
Visual Exploration of Omic Datasets Using a Shiny App
Visual Exploration of Omic Datasets Using a Shiny App
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
XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression