Biocview "DifferentialExpression"

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

Acid Genomics DESeq2 Analysis Utilities

A Comprehensive R Package For Analyzing Quantitative Phosphoproteomics Data

Active modules for multilayer weighted gene co-expression networks: a continuous optimization approach

Activity and Diversity Analysis Module Graphical User Interface

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 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 Hybrid Feature Selection method for gene expression data

Algorithms and data structures for large single-cell expression matrices

Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.

Analysis for short time-series data

Analysis of alternative poly A site usage

Analysis of alternative splicing using RNA-Seq

Analysis of Alternative Splicing Using RNA-Seq

Analysis of amplicon enrichment panels

Analysis of compositions of microbiomes with bias correction

Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account

Analysis Of Differential Abundance Taking Sample Variation Into Account

Analysis of Large Affymetrix Microarray Data Sets

Analysis of Metabolomics GC/MS Data

Analysis of Single-Cell CRISPR Screen Data

Analysis of Time-Resolved RNA-Seq Data

ANalysis Of Translational Activity (ANOTA).

Analysis of Transposable Elements

Analytical R tools for Mass Spectrometry

Analyze isomiRs and miRNAs from small RNA-seq

Analyze small RNA-seq count data

An Easy Pipeline for NanoString nCounter Data Analysis

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 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

A normalization-invariant minimum enclosing ball method to detect differentially expressed genes for RNA-seq data

An R package estimates the correlations of orthologs and transposable elements between two species

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 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 Time Course RNASeq Data Analysis

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

A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

Approximate posterior estimation for GLM coefficients

Artificial Components Detection of Differentially Expressed Genes

ascend - Analysis of Single Cell Expression, Normalisation, and Differential expression

askoR - Differential Expresion Analysis using edgeR

Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)

Assess Differential Gene Expression Experiments with ERCC Controls

a statistical framework for differential pseudotime analysis in multiple single-cell RNA-seq samples

A statistical normalization method and differential expression analysis for RNA-seq data between different species

A Tidy Transcriptomics introduction to RNA-Seq analyses

A tool for differential expression analysis and DEGs based investigation to complex diseases by bi-clustering analysis

A Tool for Generic Cell Type Enrichment Analysis

A toolkit for APA analysis using RNA-seq data

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 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

A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses

BANDITS: Bayesian ANalysis of DIfferenTial Splicing

Barycenter Single-Cell Differential Expression for Case-Control Studies

Batch Effects Quality Control Software

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 Gene eXpression

Bayesian Hidden Markov Model for the detection of differentially methylated regions

Bayesian modelling of cell-to-cell DNA methylation heterogeneity

Bayesian models for differential gene expression

Bayesian Robust Inference for Differential Gene Expression

Bcbio RNA-Seq

Benchmark of differential abundance methods on microbiome data

Bias Awared Peak Calling and Quantification for MeRIP-Seq

Big multivariate data plotted interactively

BIMEGA: BIvariate Methylation and Expression GAussian mixture model

Bioc2019PanCancerStudy

Bioconductor Web Interface

Biological Network Analysis

BLMA: A package for bi-level meta-analysis

Brings Seurat to the Tidyverse

Brings SingleCellExperiment to the Tidyverse

Brings SummarizedExperiment to the Tidyverse

Brings transcriptomics to the tidyverse

Calculates Mulcom test

cancer outlier Gene Profile Sets

Category encoding method for selecting feature genes for the classification of single-cell RNA-seq

Causal network analysis methods

Cepo for the identification of differentially stable genes

Characterization of Alternative Splicing based on Paired-End Reads

circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs

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 Time Series Gene Expression 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

Combination Connectivity Mapping

CommunityAMARETTO: A Computational Tool for the Discovery of Shared and Distinct Regulatory Mechanisms Across Biological Systems

Comparative Evaluation and Visualization of Differential Expression Analyses

Comparing Differential Abundance/Expression Methods

Comparison between multiple levels of gene expression

Comprehensive Analysis of Gene Interactivity Networks Based on Single-Cell RNA-Seq

Comprehensive analysis of transciptome data

Comprehensive analysis of transcriptome data

Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Computation of Gene Expression-Based Signatures in Breast Cancer

Compute coverage matrices from recount quickly using bwtool

Computing multi-omics driven similarity scores between patient tumor samples and cell lines for personalized medicine

ComSeq: An ensemble method for RNA-Seq differential analysis

Conditional quantile normalization

Condition specific detection from expression data

Context-Aware Transcript Quantification from Long Read RNA-Seq data

Coordinated Gene Activity in Pattern Sets

Correlation Motif Fit

Count model based differential expression and normalization on GeoMx RNA data

Covariate Assisted Large-scale Multiple testing

Create rapid visualizations of RNAseq data in R

Creation and Analysis of Pathway Expression Profiles (PEPs)

Cross Platform Meta-Analysis of Microarray Data

csSAM - cell-specific Significance Analysis of Microarrays

Cytometry Cluster Hierarchy and Cellular-to-phenotype Associations

Cytometry dATa anALYSis Tools

Data-Adaptive Statistics for High-Dimensional Multiple Testing

Data normalization by matrix raking

Data package for query/retrieval of species specific MSigDB versions

Decomposing Heterogeneous Cohorts using Omic Data Profiling

Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data

decoupleR: Ensemble of computational methods to infer biological activities from omics data

DegNorm: degradation normalization for RNA-seq data

Delineate outstanding genomic zones of differential gene activity

Denoising Algorithm based on Relevance network Topology

derfinder helper package

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

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

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 Abundant Analysis for Metabolomics and Proteomics Data

Differential Abundant Analysis for Metabolomics, Proteomics and single-cell RNA sequencing Data

Differential Alternative Polyadenylation Analysis From Compositions

Differential cell type change analysis using Logistic/linear Regression

Differential cell-type-specific allelic imbalance

Differential Co-expression Analysis

Differential co-expression/association network analysis

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 for RNA-seq data through a robust variance component test

Differential expression analysis of longitudinal count data sets

Differential Expression Analysis of NanoString nCounter Data

Differential Expression Meta-Analysis

Differential expression using kernel-based score test

Differential Expression via Distance Summary for Microarray Data

Differential gene co-expression

Differential gene expression analysis based on the negative binomial distribution

Differential Gene Expression Analysis for Multi-subject scRNA-seq

Differential gene expression data formats converter

Differential gene usage in immune repertoires

Differentially Expressed Gene-Gene pairs

Differentially Expressed Heterogeneous Overdispersion Gene Test for Count Data

Differentially regulated genes from scRNA-seq data

Differential pattern analysis for Ribo-seq data

Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq

Discriminant Analysis for Evolutionary Inference

Dispersion shrinkage for sequencing data

distinct: a method for differential analyses via hierarchical permutation tests

DNA IP-seq data analysis

doseLM

doseR

Dynamic Transcriptome Analysis

Earth Mover's Distance for Differential Analysis of Genomics Data

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

Engineering Evaluation by Gene Categorization (eegc)

Enjoy Analyzing And Integrating The Results From Differential Expression Analysis And Functional Enrichment Analysis

Enrichment Analysis using Multiple Ontologies and False Discovery Rate

Enrichment Approach to Predict Which Transcription Factors are Regulated

Ensemble of Gene Set Enrichment Analyses

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

eSVD2 for performing the eSVD-DE for cohort-wide differential expression analysis

Evaluation of normalization methods and calculation of differential expression analysis statistics

EWCE for Multiple Gene Lists

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

Explore and download data from the recount3 project

Explore and download data from the recount project

Exposome and omic data associatin and integration analysis

expression density diagnostics

Expression Weighted Celltype Enrichment

Extraction of Differential Gene Expression

FABIA: Factor Analysis for Bicluster Acquisition

Factorial designed microarray experiment analysis

Fast and Interpretable Consensus Clustering via Minipatch Learning

Fast Gene Set Enrichment Analysis

Fast Permutation-based Gene Set Analysis

FDR adjustments of Microarray Experiments (FDR-AME)

Filtering of Lowly Expressed Features

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

Fishpond: differential transcript and gene expression with inferential replicates

Fishpond: downstream methods and tools for expression data

Flexible, isoform-level differential expression analysis

For Visualizing Differential Expression 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

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

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 Meta-analysis Visualization Tool

Gene Expression Variation Analysis (GEVA)

Generally Applicable Gene-set Enrichment for Pathway Analysis

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 Quality Surrogate Variable Analysis for Degradation Correction

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 accounting for gene-gene correlations

Gene set analysis following differential expression using linear (mixed) modeling with dream

Gene Set Analysis in R

Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

Gene Set Enrichment Analysis with Networks

Gene Set Enrichment / Projection Displays

Gene Set Regulation Index

Genome-wide assessment of differential translations with ribosome profiling data

Genotype Imputed Gene Set Enrichment Analysis

GEOexplorer: a webserver for gene expression analysis and visualisation

Global Test for Counts

Global test for groups of variables via model comparisons

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 Interface for Alternative Splicing Quantification, Analysis and Visualisation

Graphical User Interface for High Performance BAM-based binary alternative splicing event quantitation, differential analysis, and visualisation

GUI for limma Package with Affymetrix Microarrays

GUI for limma Package With Two Color Microarrays

Heterogeneity-Induced Pre-Processing tOol

Heterogeneous error model for identification of differentially expressed genes under multiple conditions

Hierarchical Dependence in Meta-Analysis

Higher-Order Deconvolution Survival Analyses

High-Throughput Sequence Analysis using the Aroma Framework

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

Identifies differentially expressed genes with respect to other local genes

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 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 Intra and Inter-Donor Variations in Bulk or Single Cell Longitudinal Dataset

Identify oncogenes and tumor suppressor genes from omics data

Illumina 450K methylation array spatial analysis methods

ILoReg: a tool for high-resolution 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

Inferring unobserved perturbations from gene expression data

Integrated Differential Expression and Differential Network Analysis (INDEED)

Integrating Cap Enrichment with Transcript Expression Analysis

Integration of Microarray Data for Meta-analysis

Integrative analysis of Multi-omics data for Alternative Splicing

interactive analysis and visualization of alternative splicing in R

Interactive Analysis of Single Cell RNA-Seq Data

Interactive Differential Expresion Analysis Browser

Interactive Differential Expression AnaLysis

Interactive HTML graphics

Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection

Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package

Interval-Wise Testing for Omics Data

Introduction to Tidy Transcriptomics

Intron-Exon Retention Estimator

Investigate iLINCS for candidate repurposable drugs

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: The Smart Transcriptomic Pipeline

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

LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

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

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

Maximum Likelihood Decay Modeling of RNA Degradation Data

Mean Alterations Using Discrete Expression

Merge Maid

Meta-analysis of Gene Set differential Co-expression Analysis

Meta-analysis of RNA-Seq count data in multiple studies

Meta-Analysis of RNA-Seq Data

Meta Gene Set Co-expression Analysis

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

MethylIT utility

MethylMix: Identifying methylation driven cancer genes

Metrics to estimate a level of similarity between two ChIP-Seq profiles

Michaelis-Menten Modelling of Dropouts in single-cell RNASeq

Microarray Analysis of Differential Expression

MicroArray Chromosome Analysis Tool

Microbial Assemblage Normalized Transcript Analysis

microbiome biomarker analysis toolkit

Microbiome differential abudance and correlation analyses with bias correction

Microbiome Exploration App

Minimized Single-Cell Consensus Clustering

miRNApath: Pathway Enrichment for miRNA Expression Data

mirTarRnaSeq

Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions

MODA: MOdule Differential Analysis for weighted gene co-expression network

Model-based Analysis of Single Cell Transcriptomics

Model-Based Gene Clustering for Genomics Data from Paired/Matched Designs

Model-Based Gene Selection for Paired Data

Modeling expression drop-out for analysis of scRNA-Seq data

Modeling expression ranks for noise-tolerant differential expression analysis of scRNA-Seq data

Modularized and interactive analyses over a FacileDataStore

MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks

Multi-Contrast Gene Set Enrichment Analysis

Multi-Dataset Model-based Differential Expression Proteomics Analysis Platform

Multi matrix analysis of multiple proteomics datasets on peptide level

Multi-omics Classification, Functional Enrichment and Network Inference analysis

Multi-Omics integration and VIsualization in Cancer Subtyping

Multiple Beta t-Tests

Multiple Testing using SAM and Efron's Empirical Bayes Approaches

Multi-sample multi-group scRNA-seq data analysis tools

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 Beta t-Test

Negative Binomial Models to detect Differential Splicing

Network Perturbation Amplitude

NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment

Normal Uniform Differential Gene Expression detection

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 Protein and Phosphosite Target Identifier

Overlay omics data onto SBGN pathway diagram

Package for Fold-specific GO Terms Recognition

PAIRADISE: Paired analysis of differential isoform expression

Pairwise INTegration of functional genomics data

PatchseqMap

Pathway Analysis

Pathway Enrichment Based on Differential Causal Effects

Pathway enrichment using a regularized regression approach

PEBBA

Performance Assessment and Comparison for Survival Analysis

Perform co-DE gene analysis

Performs differential gene expression Analysis

Permutation-Based Confidence for Molecular Classification

Pipelines for Bi-Clustering Using Matrix Factorization

Platform for integrative analysis of omics data

Plotting functions for derfinder

Point Resizing for Volcano Plots

Post Translational Modification (PTM) Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

PoTRA: Pathways of Topological Rank Analysis

Power Estimation Tool for RNA-Seq and proteomics data

Preprocessing, analyzing, and reporting of RNA-seq data

Preprocessing tools for oligonucleotide arrays

Preprocessing tools for oligonucleotide arrays.

Principal Coordinates and Hotelling's T-Square method

Probabilistic Outlier Identification for RNA Sequencing Generalized Linear Models

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

Processing Various Types of Data on GEO and TCGA

Profile RA-Seq Data Using TB Pathway Signatures

Profile RNA-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

Provides shiny components to visualize multilGSEA results

Publication-ready volcano plots with enhanced colouring and labeling

Putting the fun in LINCS L1000 data analysis

QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data

Quantification and Visualization 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 drivers of variation in multilevel gene expression experiments

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

RBM: a R package for microarray and RNA-Seq data analysis

Reconstruction, visualization and analysis of branching trajectories

Reference-guided isoform reconstruction and quantification for long read RNA-Seq data

Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression

Remove Unwanted Variation from RNA-Seq Data

Report of DEG analysis

Reproducibility-Optimized Test Statistic

Reproducible GSEA Benchmarking

Resampling-based multiple hypothesis testing

Revealing differentially expressed genes using nonlinear dimensionality reduction for single cell RNA-Seq data

'rifi' analyses data from rifampicin time series created by microarray or RNAseq

R implementation of the LEfSE method for microbiome biomarker discovery

R Interface with InterMine-Powered Databases

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

RNASeqR: an R package for automated two-group RNA-Seq analysis workflow

RnaSeqSampleSize

rnaSeq secondary analyses

RNA-Seq Utilities

R Normalization and Inference of Time Series data

Robust Outlier-aware Estimation of Composition and Heterogeneity for Single-cell Data

Robust statistical inference for quantitative LC-MS proteomics

Routines for the functional analysis of biological networks

Sample Size Calculation for RNA-Seq Experimental Design

"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"

Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications

Scalable differential expression analysis of single cell transcriptomics datasets with complex study designs

Seamless navigation through combined results of set-based and network-based enrichment analysis

Shiny GATOM

Signature-based Clustering for Diagnostic Purposes

signet: Selection Inference in Gene NETworks

Significance Analysis of Function and Expression

Significance Analysis of Prognostic Signatures

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

Simulation, power evaluation, and sample size recommendation for single cell RNA-seq

Simulation tool for optimal design of high-dimensional MS-based proteomics experiment

Single-Cell Consensus Clustering

Single Cell Differential Expression

Single Cell - R Analysis Toolbox

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

Spatial transcriptome analyses of Nanostring's DSP data in R

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

Stan implementation of BASiCS

Statistical Analysis for Developmental Microarray Time Course Data

Statistical analysis for sparse high-throughput sequencing

Statistical Analysis of Molecular Profiles

Statistical Analysis of MPRA data

Statistical analysis of sequins

Statistical Analysis of the GeneChip

Statistical Characterization of Post-translational Modifications

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 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

Suffix Array Kernel Smoothing for discovery of correlative sequence motifs and multi-motif domains

Suite of Functions for Pooled Crispr Screen QC and Analysis

Summarization and expression/phenotype association of CNV ranges

Supervised Normalization of Microarrays

Switch-like differential expression across single-cell trajectories

Targeted Learning with Moderated Statistics for Biomarker Discovery

TCC: Differential expression analysis for tag count data with robust normalization strategies

TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC 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

The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)

The tidyomics blog

this package collects r fxns useful in my daily coding life

Tidy Transcriptomics for Single-cell RNA Sequencing Analyses

Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction

Time course sequencing data analysis

Tools for analyzing Micro Array experiments

Tools for Assessing Clustering

Tools for data visualization

Tools for ordering single-cell sequencing

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

Topology-based pathway analysis of RNA-seq 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

Transform Counts in RNA-Seq Data Analysis

Translational control assessment from ribosome footprint and total RNA libraries

TSS sequencing data analysis

Tumor subclonality of expression-based cancer subtypes

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

Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification

Unified statistal Modeling of Omics 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 EHT Data

Visual and interactive gene expression analysis

Visual Exploration of Omic Datasets Using a Shiny App

Visualise microarray and RNAseq data using gene ontology annotations

Wavelet-Based Models for Tiling Array Transcriptome Analysis

XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression

Yet Another Single-Cell Analysis Toolkit (Yeskit)

Biocview "DifferentialExpression"

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