Biocview "GeneExpression"

3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process

A bioconductor package for exploration of alignment gap positions from RNA-seq data

A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming

A correlation-based method for quality filtering of single-cell RNAseq data

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

Activity and Diversity Analysis Module Graphical User Interface

ADAM: Activity and Diversity Analysis Module

Adaptive Dropout Imputer (ADImpute)

Adaptive Signature Selection and InteGratioN (ASSIGN)

Add-on to DESeq to improve p-values and q-values

A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seq

A Fast Scalable and Flexible Non Negative Matrix Factorization Method

Affected pathway ranking in differential gene expression analysis

A Framework for Consensus Partitioning

A Framework for visualizing gene set enrichment throughout neurodevelopment

A Functional Approach To Impute Genetically Regulated Expression

A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC

Agreement of Differential Expression Analysis

A Hybrid Feature Selection method for gene expression data

AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype

A k-tables approach to integrate multiple Omics-Data

Alikeness Based on Regression on Transciptome DECOnvolution

alpine

A multi-tissue transcriptional age calculator

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 CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

Analysis of co-regulation and inference of 'dual regulons'

analysis of co-regulatory network motifs and inference of 'dual regulons'.

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 Large-Scale Pharmacogenomic Data

Analysis of Large-Scale Toxico-Genomic Data

Analysis of patient-derived xenograft (PDX) data

Analysis of Time-Resolved RNA-Seq Data

ANalysis Of Translational Activity (ANOTA).

Analysis of Transposable Elements

Analyze and correct probe positional bias in microarray data due to RNA degradation

An Easy Pipeline for NanoString nCounter Data Analysis

An Evolutionary Framework for the Identification and Study of Prognostic Gene Expression Signatures in Cancer

A new tool for exporting TCGA Firehose data

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

annoFuse: an R Package to annotate, prioritize, and interactively explore putative oncogenic RNA fusions

Annotation and gene expression data retrieval from Bgee database

Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology

annotation of noncoding RNAs and coexpressed genes

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

An R interface for computational modeling of tumor progression

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

An R package for DiffCircaPipeline: A framework for multifaceted characterization of differential rhythmicity

An R package for qualitative biclustering in support of gene co-expression analyses

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 creation of complex genomic profile plots

An R Package for Time Course RNASeq Data Analysis

An R package to detect chromatin state switches from epigenomic data

A package for survival time prediction based on a piecewise baseline hazard Cox regression model.

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 pipeline especially built for computing several single-cell datasets

Application of gene classifiers

Approximate posterior estimation for GLM coefficients

ArrayAnalysis

Artificial Components Detection of Differentially Expressed Genes

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

A search tool for single cell RNA-seq data by gene lists

askoR - Differential Expresion Analysis using edgeR

ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events

Assess Differential Gene Expression Experiments with ERCC Controls

Assessing the regulatory potential of DNA methylation regions or sites on gene transcription

Assessment of evidence for LOH in spatial transcriptomics pre-processed data using Bayes factor calculations

Assigning scRNA-seq to clone-of-origin using copy number from ultra-low-depth scDNA-seq

Assign Properties to TNBC Patients

Associates DNA Methylation with Matched gene Expression

Association Plots

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

A Statistical Framework for Modeling and Identifying Differential Distributions in Single-cell RNA-sequencing Data

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

A suite of functions to facilitate zFPKM transformations

A SummarizedExperiment for Ivy-GAP data

A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data

A Supervised Approach for Predicting Cell Cycle Progression Using Single-Cell RNA-seq Data

Asymmetric Within-Sample Transformation

A Systems Biology Approach for Drug Repurposing

A Tidy Transcriptomics introduction to RNA-Seq analyses

A time series clustering package combining slope and Frechet distances

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 tool for unsupervised projection of single cell RNA-seq data

A toolkit for APA analysis using RNA-seq data

a tool set for pathway based data integration and visualization

A Tool to Analyze and Design NGS Based Custom Gene Panels

A tool to use GO Subtrees to Tag and Annotate Genes within a set

AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)

A unified interface to a plethora of gene set enrichment analysis methods

Automated Affymetrix Array Analysis Classification Package

Automated analysis of high-throughput qPCR data

Automated functions for comparing various omic data from cbioportal.org

Automated, probabilistic assignment of scRNA-seq to cell types

Automatic calculation of literature relevance of genes

Automatic RNA-Seq present/absent gene expression calls generation

A visualization tool for single cell data of C.elegans embrogenesis

A web interface for gene-set enrichment analyses

A work flow for analysis and normalization of pre-processing RT-qPCR data

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

BANDITS: Bayesian ANalysis of DIfferenTial Splicing

Base NanoString Experiment Class

Base package for enabling powerful shiny web displays of Bioconductor objects

Batch Effects Correction with Unknown Subtypes

Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments

Bayesian Analysis of Single-Cell Sequencing data

Bayesian clustering and imputationa of single cell methylomes

Bayesian Hidden Markov Model for the detection of differentially methylated regions

Bayesian hierarchical mixture of factor analyzers for modelling genomic bifurcations

Bayesian Inference of Regulation of Transcriptional Activity

Bayesian Inference of Regulatory Influence on Expression (biRte)

Bayesian modelling of cell-to-cell DNA methylation heterogeneity

BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data

Benchmarking of several gene network inference methods

Better prediction by use of co-data: Adaptive group-regularized ridge regression

Big multivariate data plotted interactively

BIMEGA: BIvariate Methylation and Expression GAussian mixture model

Binding site defintion based on iCLIP data

Bioc2019PanCancerStudy

Bioconductor components for general cancer genomics

Biological Network Analysis

Biological Network Reconstruction Omnibus

BioTIP: An R package for characterization of Biological Tipping-Point

Brain Span Atlas in Biobase Expressionset R toolset

Brings Seurat to the Tidyverse

Brings SingleCellExperiment to the Tidyverse

Brings SummarizedExperiment to the Tidyverse

Brings transcriptomics to the tidyverse

Building Expression Atlas from RNA-Seq data

Calculates Mulcom test

Cancer subtypes identification, validation and visualization based on multiple genomic data sets

Candidate Driver Analysis

Candidate Gene Miner

Candidate gene prioritization based on convergent evidence

Casc

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

CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data

Cell-Cycle using Mixture Models

Cell OrderiNg by FluorEScence Signal

CellRanger Input/Output

Cell type annotation for unannotated single-cell RNA-Seq data

Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms

CEllular Latent Dirichlet Allocation

Cepo for the identification of differentially stable genes

ceRNAR: An R Package for Identification and Analysis of ceRNAs-miRNA Triplets

Characterization of Alternative Splicing based on Paired-End Reads

CHARGE: CHromosome Assessment in R from Gene Expression data

Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata

Chromosmal Aberrations Finder in Expression data

CiteFuse: multi-modal analysis of CITE-seq data

Classification of alternative splicing and prediction of coding potential from RNA-seq data.

Classifier for Single-cell RNA-seq Using Cell Clusters

Classify Samples From RNA-Seq Datasets

Client for the Reactome Analysis Service for comparative multi-omics gene set analysis

Clone Identification from Single Cell Data

Clustering Algorithms for Bioconductor

Clustering and Resolution Enhancement of Spatial Transcriptomes

Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models

Clustering approach to solve complete Deconvolution problem

Clustering Comparison Package

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

CMap Tools in R

CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models

Codon Usage Analysis and Prediction of Gene Expressivity

coexnet: An R package to build CO-EXpression NETworks from Microarray Data

co-expressed gene-set enrichment analysis

Co-Expression Analysis of Sequencing Data

Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis

Co-expression Modules identification Tool

co-expression of lincRNAs and protein-coding genes

COexpression Tables ANalysis

Combination Connectivity Mapping

Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)

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

Comparison of disease and drug profiles using Gene set Enrichment Analysis

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

Computational pipeline for computing probability of modification from structure probing experiment data

Computation of Gene Expression-Based Signatures in Breast Cancer

Compute coverage matrices from recount quickly using bwtool

Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs

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

Concomitant identification of distinctness and similarity in gene expression analysis.

Constructing gene regulatory networks from expression data through functional module inference

Contains utils for loading and manipulating two-layers structure network models

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

Convex Analysis of Mixtures for Tissue Heterogeneity Characterization

Convex Analysis of Mixtures Version 3

Coordinated Gene Activity in Pattern Sets

CoRegFlux

CoRegNet : reconstruction and integrated analysis of co-regulatory networks

Correspondence Analysis for Single Cell Data

Count model based differential expression and normalization on GeoMx RNA data

Count summarization and normalization for RNA-Seq data

Covariate Assisted Large-scale Multiple testing

Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them

Create rapid visualizations of RNAseq data in R

Creates and uses physio spaces as a dimension reduction mapping

Creation and Analysis of Pathway Expression Profiles (PEPs)

Cross-platform consensus analysis of genomic measurements via interlaboratory testing method

Cross Platform Meta-Analysis of Microarray Data

Cross Platform Omics Prediction

Data-Adaptive Statistics for High-Dimensional Multiple Testing

Data-driven normalization strategies for high-throughput qPCR data.

Data for the alpine package vignette

Data package for query/retrieval of species specific MSigDB versions

Data Package for the annoFuse Bioconductor Package

Decomposing Heterogeneous Cohorts using Omic Data Profiling

Deconvolution by Convex Analysis of Mixtures

Deconvolution of mixed cells from spatial and/or bulk gene expression 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

DeMAND

Denoising Algorithm based on Relevance network Topology

Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm

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 hidden batch factors through data adaptive adjustment for biological effects

Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decomposition

Detection of miRNAs that regulate interacting groups of pathways

Detect tissue heterogeneity in expression profiles with gene sets

DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates

dgeAnalysis

Differential cell type change analysis using Logistic/linear Regression

Differential cell-type-specific allelic imbalance

Differential Co-expression Analysis

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 Meta-Analysis

Differential expression using kernel-based score test

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

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

Different methods for the integrative analysis multiple omics data

Diffusion scores on biological networks

diffUTR: Streamlining differential exon and 3' UTR usage

Discriminant Analysis for Evolutionary Inference

Dispersion shrinkage for sequencing data

Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles

distinct: a method for differential analyses via hierarchical permutation tests

doseR

Dry lab for exploring miRNA-mRNA relationships

Dynamic Transcriptome Analysis

Earth Mover's Distance for Differential Analysis of Genomics Data

Easy Analysis of RNASeq DE

EasyqpcR for low-throughput real-time quantitative PCR data analysis

ELBOW - Evaluating foLd change By the lOgit Way

Empirical Analysis of Digital Gene Expression Data in R

Empirical Bayes estimate of block diagonal covariance matrices

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

Epigenomic tools

EpiMethEx Package

EpiMix: an integrative tool for the population-level analysis of DNA methylation

Estimate Promoter Activity from RNA-Seq data

Estimate Systems Immune Response from RNA-seq data

Estimation of genetic and molecular regulatory networks from high-throughput genomics data

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

Evaluate Cellspecific Mixing

EWCE for Multiple Gene Lists

Example experimental microarray data set for the "biotmle" R package

Exon Based Strategy for Expression Analysis of genes

Exon-Intron Split Analysis (EISA) in R

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 data analysis via the Iterative Signature Algorithm

Expression Weighted Celltype Enrichment

Extraction of Differential Gene Expression

Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data

Factor Loading Adaptive SHrinkage in R

FARMS - Factor Analysis for Robust Microarray Summarization

Fast Correlation Based Filter for Feature Selection

Fast Gene Set Enrichment Analysis

Fast Permutation-based Gene Set Analysis

FCBF-based Co-Expression Networks for Single Cells

Filtering of Lowly Expressed Features

Filter replicated high-throughput transcriptome sequencing data

Find Causal Cell-Types Underlying Complex Trait Genetics

Finding an Active Metabolic Module in Atom Transition Network

Finding differentially expressed unannotated genomic regions from RNA-seq data

Find Potential Disease-Related Genes

Find the most characteristic gene ontology terms for groups of human genes

Fishpond: differential transcript and gene expression with inferential replicates

Fishpond: downstream methods and tools for expression data

Fit transcriptional regulatory networks using gene expression, priors, machine learning

Flexible, probabilistic metrics for quality control of scRNA-seq data

For Visualizing Differential Expression Analysis

Functional annotation-driven unsupervised clustering for single-cell data

Functional interpretation of single cell RNA-seq latent manifolds

Functionality to Read and Manipulate SomaLogic ADAT files

Functional Network Analysis

Functional similarities

functions for genome-wide application of Liquid Association

Functions for normalisation of RT-qPCR data

Functions used to preprocess datasets stored in BioDataome

Functions useful for those doing repetitive analyses with Affymetrix GeneChips

GAPGOM (novel Gene Annotation Prediction and other GO Metrics)

GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC

GEM: fast association study for the interplay of Gene, Environment and Methylation

Genearting Samples of Gene Expression Data with Variational Autoencoders

Gene Expression Atlas query and gene set enrichment package.

Gene expression-based subtype classification for high-grade serous ovarian cancer

Gene expression changes in three biological conditions

Gene expression enrichment in human brain regions

Gene Expression Meta-analysis Visualization Tool

Gene Expression Signature based Similarity Metric

Gene Expression Variation Analysis (GEVA)

GEne Network Inference with Ensemble of trees

Gene Ontology analyser for RNA-seq and other length biased data

Generally Applicable Gene-set Enrichment for Pathway Analysis

Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq

General Sample Size and Power Analysis for Microarray and Next-Generation Sequencing Data

Generating Tree Hierarchy Visualizations from Gene Expression Data

Gene regulator enrichment analysis

Gene Regulatory Network Inference Using Time Series

Gene set analysis accounting for gene-gene correlations

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

Gene Set Enrichment Analysis Extended to Contingency Cubes

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

Gene Set Enrichment Analysis with Networks

Gene set enrichment data structures and methods

Gene Set Regulation (GS-Reg)

Genomic Instability estimation for scRNA-Seq

Genomic trajectories with heterogeneous genetic and environmental backgrounds

Genotype Imputed Gene Set Enrichment Analysis

GEOexplorer: a webserver for gene expression analysis and visualisation

Global Test for Counts

goProfiles: an R package for the statistical analysis of functional profiles

GPA (Genetic analysis incorporating Pleiotropy and Annotation)

GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data

graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture

Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

GSCA: Gene Set Context Analysis

GUI for limma Package with Affymetrix Microarrays

GUI for limma Package With Two Color Microarrays

Heatmaps of Stack Profiles from Epigenetic Signals

Helper Functions for LIBD Deconvolution

Heterogeneity-Induced Pre-Processing tOol

Hi-C Annotation and Graphics Ensemble

Higher-Order Deconvolution Survival Analyses

High-Throughput Sequence Analysis using the Aroma Framework

HiPathia: High-throughput Pathway Analysis

HTSanalyzeR2: An R package for functional annotation, network analysis and time series analysis of high-throughput data

Hybrid Multiple Testing

Identification and Analysis of ceRNA Regulation

Identification and analysis of miRNA sponge interaction networks and modules

Identification and analysis of miRNA sponge regulation

Identification of candidate causal perturbations from differential gene expression data

Identification of cell-type-specific spatially variable genes accounting for excess zeros

Identification of CTC in Blood Streams

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 genes associated with multiple expression phenotypes in single-cell CRISPR screening data

Identifying Genes Overexpressed in Subsets of Tumors from Tumor-Normal mRNA Expression Data

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

Identify likely duplicate samples from genomic or meta-data

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

Implementation of gene expression anti-profiles

Import and summarize transcript-level estimates for transcript- and gene-level analysis

Improving replicability in single-cell RNA-Seq cell type discovery

Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis

Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure

Inference of differential exon usage in RNA-Seq

Inference of gene regulatory networks from gene expression data

Inference of Genetic Variants Driving Cellular Phenotypes

Inferring miRNA sponge modules in heterogeneous data

Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

Inferring the Tree of Cells

Inferring unobserved perturbations from gene expression data

Infers biological signatures from gene expression data

In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data

integrated Bayesian Modeling of eQTL data

Integrating Cap Enrichment with Transcript Expression Analysis

Integrative analysis of Multi-omics data for Alternative Splicing

Integrative analysis of multi-omics data to infer regulatory networks

Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection

Integrative Statistics of alleLe Dependent Expression

Interactive Analysis of Single Cell RNA-Seq Data

Interactive Differential Expresion Analysis Browser

Interactive Differential Expression AnaLysis

Interactive HTML graphics

Interactive Multi-Omics Cancers Data Visualization and Analysis

Interactive SummarizedExperiment Explorer

Interactive visualization of scRNA-seq data with Cerebro

Interpretable marker-based single-cell pseudotime using Bayesian parametric models

Interspecies gene mapping

Introduction to Tidy Transcriptomics

iPath pipeline for detecting perturbed pathways at individual level

iSEE Universe

Judging Quality of Clustering Methods using Mutual Information

KMPPc: K-M Plot for Pan-cancer

KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline

Landscape Expression Visualization Interface

Landscape Single Cell Entropy

Laplacian eigenmaps & principal curves for pseudotemporal ordering of single-cell RNA-seq data

Learn and Apply Cell Type Signatures

Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level

Linear model and normality based normalization and transformation method (Linnorm)

Linear Models for Microarray Data

Linear Subpsace identification to solve complete gene expression deconvolution problem

LiquidAssociation

Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs

Long gene expression as a metric for neuronal identity

LPEseq: local-pooled-error test for RNA-seq data with a small number of replicates

Machine learning tools for automated transcriptome clustering analysis

Make read coverage plots from BigWig files

Mapping, quantification and variant analysis of sequencing data

Marker Gene Finder in Microarray gene expression data

Marker Gene Finder in RNA-seq data

masan uses bioconductor to analyze microarray data

massiR: MicroArray Sample Sex Identifier

Massive and Integrative Gene Set Analysis

Massive correlating biclusters for gene expression data and associated methods

Mass Spectrometry-Based Single-Cell Proteomics Data Analysis

Maximum Likelihood Decay Modeling of RNA Degradation Data

Mean Alterations Using Discrete Expression

MetaAnalysis for High Throughput Experiments

Meta-analysis of high-throughput experiments using feature annotations

Meta-Analysis of High-Throughput Experiments Using Feature Annotations

Methods for Single-Cell RNA-Seq Data Analysis

Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape

Methylation array and sequencing spatial analysis methods

MethylMix: Identifying methylation driven cancer genes

Michaelis-Menten Modelling of Dropouts in single-cell RNASeq

Microarray Analysis of Differential Expression

Microbial Assemblage Normalized Transcript Analysis

Mine Associated Gene Expressions (from single-cell Rna Seq data)

Mini-batch K-means Clustering for Single-Cell RNA-seq

miRDriver: A Tool to Infer Copy Number Derived miRNA-Gene Networks in Cancer

MiRNA Ranking by Gene Expression

Mixture Nested Effects Models

MLG Clustering

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

Model-based Analysis of Single Cell Transcriptomics

Model higher-order methylation profiles

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

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

Modeling networks for individual samples using LIONESS

Modeling Network State Transitions from Expression and Regulatory data (MONSTER)

Modularized and interactive analyses over a FacileDataStore

Monte Carlo Reference-based Consensus Clustering

multiClust: An R-package for Identifying Biologically Relevant Clusters in Cancer Transcriptome Profiles

Multi-Contrast Gene Set Enrichment Analysis

Multiomic Batch effect Correction

Multiple Beta t-Tests

Multiple omics data integrative clustering and gene set analysis

Multiple Testing using SAM and Efron's Empirical Bayes Approaches

Multi-Scale Target Explorer

Multivariate analysis of microarray data using ADE4

Multivariate Analysis of Transcriptomic Data

NanoString data normalization and differential gene expression analysis

NanoString GeoMx Tools

NanoString nCounter Tools

Negative Binomial Additive Model for RNA-Seq Data

Negative Binomial Beta t-Test

Negative binomial model for scRNA-seq

Neighbor_net analysis

Network Perturbation Amplitude

Network smoothing for scRNAseq

NEUral network-based single-Cell Annotation tool

Non-detects in qPCR data

Normalization of Single-Cell mRNA Sequencing Data

Obtain Raw Read Counts from RNASeq Data

Open Cancer TherApeutic Discovery (OCTAD)

Optimising the Definition of Expressed Regions

Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq

Outlier Analysis for pairwise differential comparison

Outlier-aware and Count-based Compositional Analysis of Single-cell Data.

Outlier Gene Set Analysis

outlier methods with applications in cancer

Outlier profile and pathway analysis in R

Outlier Protein and Phosphosite Target Identifier

OUTRIDER - OUTlier in RNA-Seq fInDER

Overlay omics data onto SBGN pathway diagram

OVESEG-test to detect tissue/cell-specific markers

Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection

Package for enabling powerful shiny web displays of Bioconductor objects

Package for Fold-specific GO Terms Recognition

Package to Perform High Throughput Biological Screening

Package to work with miRNAs and miRNA targets with R

Packaging common Seurat analysis tasks

Pairwise INTegration of functional genomics data

Pancreatic Ductal Adenocarcinoma Tool-Kit

PANDA Algorithm

PatchseqMap

Pathway Enrichment Analysis Based on Bayesian Network

Pathway Enrichment Based on Differential Causal Effects

Pathway enrichment using a regularized regression approach

Pathway fingerprinting for analysis of gene expression arrays

Pathway RespOnsive GENes for activity inference from gene expression

pcaGoPromoter is used to analyze DNA micro array data

PCAtools: Everything Principal Components Analysis

Performance Assessment and Comparison for Survival Analysis

Perform co-DE gene analysis

Permutation-Based Confidence for Molecular Classification

pipeComp pipeline benchmarking framework

Pipeline for augmented co-expression analysis

Pipeline for single cell multi-omic data pre-processing

pipeline for single cell RNA-seq data analysis

Platform for integrative analysis of omics data

plot bayesian network inferred from gene expression data based on enrichment analysis results

Point Resizing for Volcano Plots

PolyA counting and differential transcript usage analysis for scRNA-seq data

Position Related Data Analysis

PoTRA: Pathways of Topological Rank Analysis

Predict genes expressed selectively in specific cell types

Predicting Targets for Drosophila Intragenic miRNAs

Pre-Processing for HIPC ImmuneSignatures2 Analysis

Preprocessing tools for oligonucleotide arrays

Preprocessing tools for oligonucleotide arrays.

Pretrained learning models for cell type prediction on single cell RNA-sequencing data

Principal Coordinates and Hotelling's T-Square method

Prize: an R package for prioritization estimation based on analytic hierarchy process

Probabilistic Outlier Identification for RNA Sequencing Generalized Linear Models

PRObabilistic Pathway Score (PROPS)

Probe-level Expression Change Averaging

Probe region expression estimation for RNA-seq data for improved microarray comparability

Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

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

Programmatic access to the DEE2 RNA expression dataset

Projection onto Orthogonal Space Testing for High Dimensional Data

PRojection Onto the Most Interesting Statistical Evidence

PROMISE analysis with Canonical Correlation for Two Forms of High Dimensional Genetic Data

Promoter identification from large-scale TSS profiling data

Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)

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

Quality assessment and control for FFPE microarray expression data

Quality Control for Single-Cell RNA-seq Data

Quality Control of Normalized Gene Expression Data

Quantification of the Tumor Immune contexture from RNA-seq data

Quantify and interpret divers of variation in multilevel gene expression experiments

Quantify and interpret drivers of variation in multilevel gene expression experiments

Queries the Human Protein Atlas Staining Data for Multiple Proteins and Genes

Random Rotation Methods for High Dimensional Data with Batch Structure

Rank-based signature enrichment analysis for single-cell data

Rank-based single-sample gene set scoring method

Rank Product method for identifying differentially expressed genes with application in meta-analysis

Rapid Reconstruction of Time-Varying Gene Regulatory Networks

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/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts

RBioinf

rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines

Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets

Read qPCR data

Reconstruction, visualization and analysis of branching trajectories

Recovering spatially-varying cell-specific gene co-expression networks for single-cell spatial expression data.

Reference-Based Single-Cell RNA-Seq Annotation

Reference-free Cell-Type Deconvolution of Multi-Cellular Spatially Resolved Transcriptomics Data

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

Regression-based network inference using Bayesian Model Averaging

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

regutools: an R package for data extraction from RegulonDB

Removal of unwanted variation for gene-gene correlations and related analysis

Report of DEG analysis

Representing Different Biological Sets

Reproducibility-Optimized Test Statistic

Reproducible GSEA Benchmarking

R functions for the normalization of Exiqon miRNA array data

R implementation of Information measures

R implementation of informtion measures

R Interface with InterMine-Powered Databases

RNA-binding protein motif analysis

RNAseq and qPCR signal comparison

RNA-Seq multi-mapping Reads Quantification Tool

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

Routines for the functional analysis of biological networks

R package for RIVER (RNA-Informed Variant Effect on Regulation)

R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data

R package motivated by the SCTC Dream Challenges

RPA: Robust Probabilistic Averaging for probe-level analysis

rRice package to make easier the study of the genomic of rice

RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons

runibic: row-based biclustering algorithm for analysis of gene expression data in R

Run `magic-impute` on scRNA Seq dataset in R

S4 Class for Spatially Resolved -omics Data

samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulation

Sample Classifier

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

Scalable identification of spatially variable genes in spatially-resolved transcriptomics data

Scaling normalization based on the Pareto distribution

scClassify: single-cell Hierarchical Classification

scDataviz: single cell dataviz and downstream analyses

sciCNV

scMerge: Merging multiple batches of scRNA-seq data

scraps output import and processing in R

scRecover for imputation of single-cell RNA-seq data

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

Search for correlation between epigenetic signals and gene expression in TADs

sechm: Complex Heatmaps from a SummarizedExperiment

Semi-parametric simulation tool for bulk and single-cell RNA sequencing data

Semi-supervised adaptive-height snipping of the Hierarchical Clustering tree

SEPA

SEtools: tools for working with SummarizedExperiment

Shiny GATOM

sigFeature: Significant feature selection using SVM-RFE & t-statistic

Signature-based Clustering for Diagnostic Purposes

signet: Selection Inference in Gene NETworks

Significance Analysis of Prognostic Signatures

Similarity Identification in Gene Expression

SIMLR: Single-cell Interpretation via Multi-kernel LeaRning

Simple Simulation of Single-cell RNA Sequencing Data

Simplified RNA-Seq Analysis Pipeline

Simulation and Deconvolution of Omic Profiles

Single-cell analysis toolkit for gene expression data in R

Single-Cell Analysis Toolkit for Gene Expression Data in R

Single-Cell Batch Correction Methods

Single-Cell Data Visualisation Using Kernel Gene-Weighted Density Estimation

Single Cell Entropy

single-cell higher order testing

Single Cell Inference of Regulatory Activity

Single-cell Interpretation via Multi-kernel LeaRning (SIMLR)

Single Cell Overview of Normalized Expression data

Single Cell Pipeline

Single Cell - R Analysis Toolbox

Single cell replicability analysis

Single-Cell RNA-Seq Analysis Utilities

Single-Cell RNA-Seq Utilities

Single Cell Shiny Application for Analysing Single Cell Transcriptomics Data

Single-cell Targetted Network Inference

Single-Cell Trajectory Analysis Utilities

Single-gene classifiers and outlier-resistant detection of differential expression for two-group and survival problems

Small-Count Analysis Methods for High-Dimensional Data

small RNA-Seq Utilities

software and data for analyses in genetics of gene expression

Sparse Contrastive Principal Component Analysis

Sparse Partial Correlations On Gene Expression

spatialHeatmap

Spatial Overlay for Omic Data from Nanostring GeoMx Data

Spatial transcriptome analyses of Nanostring's DSP data in R

Spatial transcriptomic clustering

Spatial Transcriptomics Analysis

SPIA-PCC: Signaling pathway impact analysis incorporated the change of Pearson correla-tion coefficient between two groups

Splice Interpreter of Transcripts

SpotClean adjusts for spot swapping in spatial transcriptomics data

ssPATHS: Single Sample PATHway Score

Standardize Antibody Names

Stan implementation of BASiCS

Statistical Analysis of MPRA data

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 based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)

Statistical methods for analysing single cell RNA-seq data

Statistics for Integrative Genomics Analyses in R

Strength of Selected Codon Usage

Structure Learning for Count Data

Subsampling of high-throughput sequencing count data

Subtype Identification with Survival Data

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

Summarization and expression/phenotype association of CNV ranges

Supervised Normalization of Microarrays

supraHex: a supra-hexagonal map for analysing tabular omics data

Survival analysis for gene signatures

SVAPLSseq-An R package to estimate the hidden factors of unwanted variability and adjust for them to enable a more powerful and accurate differential expression analysis based on RNAseq data

Switch-like differential expression across single-cell trajectories

Synthetic Expression Data for Gene Regulatory Network Inference

systemPipeRdata: Workflow templates and sample data

systemPipeR: NGS workflow and report generation environment

systemPipeR: Workflow Environment for Data Analysis and Report Generation

Systems biology tool to simulate gene regulatory circuits

Systems EPigenomics Inference of Regulatory Activity

Targeted Learning with Moderated Statistics for Biomarker Discovery

T-cell Receptor/Immunoglobulin Profiler (TRIP)

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

"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"

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

This Package Discovers Directionality in Time and Pseudo-times Series of Gene Expression Patterns

This R package for performing module repertoire analyses and generating fingerprint representations

Tidy Transcriptomics for Single-cell RNA Sequencing Analyses

Tidyverse functions for SummarizedExperiment

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

Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines

Tissue-specific gene enrichment analysis

TNBC.CMS: Prediction of TNBC Consensus Molecular Subtypes

Tokenizing Text of Gene Set Enrichment Analysis

Tomo-seq data analysis

Tool for Evaluation of Cell Identity from Transcription Profiles

Toolkit for Single-Cell Velocity

Toolkit for the automatic analysis of omics data

Tools for Assessing Clustering

Tools for computational epigenomics

Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data

Tools for Managing Seurat Objects

Tools for manipulating GO and microarrays

Tools for matrices with precision weights, test and explore weighted or sparse data

Tools for ordering single-cell sequencing

Tools for Single-Cell Analysis

Tools for the analysis of heterogeneous tissues

Tools for the Efficient Analysis of High-Resolution Genomics Data

Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level

Top Confident Effect Sizes

Topology-based pathway analysis of RNA-seq data

Training of logical models from indirect measurements of perturbation experiments

trajectory-based differential expression analysis for sequencing data

Trajectory functions for visualization and interpretation.

Transcript expression inference and differential expression analysis for RNA-seq data

Transcriptional analysis based on transcriptograms

Transcriptional Data Guided fMRI Network Classification

Transcriptional Regulatory Inference from Genetics of Gene ExpRession

Transcription factor Inference through Gaussian process Reconstruction of Expression

Transcriptome instability analysis

Transcriptomic Ovarian Cancer Datasets

Transcript Quantification Import with Automatic Metadata

Translational control assessment from ribosome footprint and total RNA libraries

TSCAN: Tools for Single-Cell ANalysis

TSS sequencing data analysis

Tumor heterogeneity level evaluation

Tumor subclonality of expression-based cancer subtypes

Turn Bioconductor objects into tidy data frames

Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis

Unbiased Extraction of Single Cell Identity using Multiple Correspondence Analysis

Unified methods for the inference and analysis of gene regulatory networks

Unified statistal Modeling of Omics Data

Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data

Unlocking iSEE for transcript-level visualization

Unsupervised Identification of Genes with Expression Loss in Subsets of Tumors

User Friendly Single-Cell and Bulk RNA Sequencing Visualization

Uses Brown's method to combine p-values from dependent tests

Utilities for Handling Single-Cell Droplet Data

Variance Adaptive Shrinkage

Varying-Censoring Aware Matrix Factorization

VeloViz: RNA-velocity informed 2D embeddings for visualizing cell state trajectories

VirtUaL ChIP-Seq data Analysis using Networks

Virtual Inference of Protein-activity by Enriched Regulon analysis

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 correlation results and test significancies of these

Visualise microarray and RNAseq data using gene ontology annotations

Visualising Set Enrichment Analysis Results

Visualization functions for spatial transcriptomics data

Visualize all edges within a KEGG pathway and overlay LINCS data

Visualize all edges within a KEGG pathway and overlay LINCS data [option]

Visualize biclusters identified in gene expression data

Wavelet-Based Models for Tiling Array Transcriptome Analysis

What the Package Does (One Line, Title Case)

What the Package Does TODOELI

Word cloud summaries of GO enrichment analysis

xcore expression regulators inference

YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization

Yet Another Single-Cell Analysis Toolkit (Yeskit)

Zero-Inflated Negative Binomial Model for RNA-Seq Data

Biocview "GeneExpression"

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