Biocview "GeneExpression"

3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process
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 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 CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming
A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming
Acid Genomics GSEA
Acid Genomics GSEA
Acid Genomics GSEA
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
Active modules for multilayer weighted gene co-expression networks: a continuous optimization approach
Adaptive Signature Selection and InteGratioN (ASSIGN)
Adaptive Signature Selection and InteGratioN (ASSIGN)
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 dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seq
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 Consensus Partitioning
A Framework for visualizing gene set enrichment throughout neurodevelopment
A Framework for visualizing gene set enrichment throughout neurodevelopment
A Functional Approach To Impute Genetically Regulated Expression
A Functional Approach To Impute Genetically Regulated Expression
A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC
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
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
A k-tables approach to integrate multiple Omics-Data
Alikeness based on Regression on Transciptome DECOnvolution
Alikeness based on Regression on Transciptome DECOnvolution
alpine
alpine
A Minimum Enclosing Ball (MEB) method to detect differential expression genes for RNA-seq data
A multi-tissue transcriptional age calculator
A multi-tissue transcriptional age calculator
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 CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
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 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 co-regulatory network motifs and inference of 'dual regulons'.
analysis of co-regulatory network motifs and inference of 'dual regulons'.
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 Large-Scale Pharmacogenomic Data
Analysis of Large-Scale Pharmacogenomic Data
Analysis of Large-Scale Pharmacogenomic Data
Analysis of Large-Scale Toxico-Genomic Data
Analysis of patient-derived xenograft (PDX) data
Analysis of patient-derived xenograft (PDX) 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
Analyze and correct probe positional bias in microarray data due to RNA degradation
A new tool for exporting TCGA Firehose data
A new tool for exporting TCGA Firehose data
An integrated analysis package of Gene expression and Copy number alteration
An integrated analysis package of 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 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 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 interface for computational modeling of tumor progression
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 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 creation of complex genomic profile plots
An R package for the creation of complex genomic profile plots
An R package to detect chromatin state switches from epigenomic data
An R package to detect chromatin state switches from epigenomic data
An R package to detect chromatin state switches from epigenomic data
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
Application of gene classifiers
Application of gene classifiers
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
A search tool for single cell RNA-seq data by gene lists
A search tool for single cell RNA-seq data by gene lists
ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events
ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events
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
Assigning scRNA-seq to clone-of-origin using copy number from ultra-low-depth scDNA-seq
Assign Properties to TNBC Patients
Assign Properties to TNBC Patients
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 suite of functions to facilitate zFPKM transformations
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 **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data
A Systems Biology Approach for Drug Repurposing
A time series clustering package combining slope and Frechet distances
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 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 unsupervised projection of single cell RNA-seq data
A tool for unsupervised projection of single cell RNA-seq data
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 Analyze and Design NGS Based Custom Gene Panels
A Tool to Analyze and Design NGS Based Custom Gene Panels
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
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)
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 analysis of high-throughput qPCR data
Automated functions for comparing various omic data from cbioportal.org
Automated functions for comparing various omic data from cbioportal.org
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 calculation of literature relevance of genes
Automatic calculation of literature relevance of genes
Automatic calculation of literature relevance of genes
Automatic RNA-Seq present/absent gene expression calls generation
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
BANDITS: Bayesian ANalysis of DIfferenTial Splicing
BANDITS: Bayesian ANalysis of DIfferenTial Splicing
Base package for enabling powerful shiny web displays of Bioconductor objects
Base package for enabling powerful shiny web displays of Bioconductor objects
Base package for enabling powerful shiny web displays of Bioconductor objects
Batch Effects Correction with Unknown Subtypes
Batch Effects Correction with Unknown Subtypes
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 Single-Cell Sequencing data
Bayesian Analysis of Single-Cell Sequencing data
Bayesian clustering and imputationa of single cell methylomes
Bayesian clustering and imputationa of single cell methylomes
Bayesian hierarchical mixture of factor analyzers for modelling genomic bifurcations
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)
BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data
BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data
bcbio RNA-Seq
bcbio RNA-Seq
Benchmarking of several gene network inference methods
Benchmarking of several gene network inference methods
Benchmarking of several gene network inference methods
Better prediction by use of co-data: Adaptive group-regularized ridge regression
Better prediction by use of co-data: Adaptive group-regularized ridge regression
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 components for general cancer genomics
Bioconductor components for general cancer genomics
Biological Network Analysis
Biological Network Analysis
BioTIP: An R package for characterization of Biological Tipping-Point
BioTIP: An R package for characterization of Biological Tipping-Point
BioTIP: An R package for characterization of Biological Tipping-Point
Brain Span Atlas in Biobase Expressionset R toolset
Calculates Mulcom test
Cancer subtypes identification, validation and visualization based on multiple genomic data sets
Cancer subtypes identification, validation and visualization based on multiple genomic data sets
Candidate gene prioritization based on convergent evidence
Candidate gene prioritization based on convergent evidence
Candidate gene prioritization based on convergent evidence
Candidate gene prioritization based on convergent evidence
Casc
CB2: A cluster-based approach for distinguishing cells from background barcodes in 10x Genomics data
Cell-Cycle using Mixture Models
Cell OrderiNg by FluorEScence Signal
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
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
CEllular Latent Dirichlet Allocation
CEllular Latent Dirichlet Allocation
Characterization of Alternative Splicing based on Paired-End Reads
CHARGE: CHromosome Assessment in R from Gene Expression data
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
CiteFuse: multi-modal analysis of CITE-seq data
Classification of alternative splicing and prediction of coding potential from RNA-seq data.
Classify Samples From RNA-Seq Datasets
Client for the Reactome Analysis Service for comparative multi-omics gene set analysis
Client for the Reactome Analysis Service for comparative multi-omics gene set analysis
Clone Identification from Single Cell Data
Clone Identification from Single Cell Data
Clustering and Visualizing RNA-Seq Expression Data using Grade of Membership Models
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 high-throughput sequencing data by identifying co-expression patterns
Clustering of Time Series Gene Expression data
Clustering of Time Series Gene Expression data
CMap Tools in R
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
Codon Usage Analysis and Prediction of Gene Expressivity
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
co-expressed gene-set enrichment analysis
co-expressed gene-set enrichment analysis
Co-Expression Analysis of Sequencing Data
Co-Expression Analysis of Sequencing Data
Co-Expression Analysis of Sequencing 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
Co-expression Modules identification Tool
Co-expression Modules identification Tool
co-expression of lincRNAs and protein-coding genes
co-expression of lincRNAs and protein-coding genes
Combination Connectivity Mapping
Combination Connectivity Mapping
Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)
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
Comparing Differential Abundance/Expression Methods
Comparison between multiple levels of gene expression
Comparison of disease and drug profiles using Gene set Enrichment Analysis
Comparison of disease and drug profiles using Gene set Enrichment Analysis
Comprehensive analysis of transciptome data
Comprehensive analysis of transcriptome data
Computational pipeline for computing probability of modification from structure probing experiment data
Computational pipeline for computing probability of modification from structure probing experiment 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
Computes the Quaternary Dot Product Scoring Statistic for Signed and Unsigned Causal Graphs
ComSeq: An ensemble method for RNA-Seq differential analysis
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
Constructing gene regulatory networks from expression data through functional module inference
Constructing gene regulatory networks from expression data through functional module inference
Contains utils for loading and manipulating two-layers structure network models
Contains utils for loading and manipulating two-layers structure network models
Contains utils for loading and manipulating two-layers structure network models
Convex Analysis of Mixtures for Tissue Heterogeneity Characterization
Convex Analysis of Mixtures for Tissue Heterogeneity Characterization
Coordinated Gene Activity in Pattern Sets
Coordinated Gene Activity in Pattern Sets
CoRegFlux
CoRegFlux
CoRegNet : reconstruction and integrated analysis of co-regulatory networks
CoRegNet : reconstruction and integrated analysis of co-regulatory networks
CoRegNet : reconstruction and integrated analysis of co-regulatory networks
Count summarization and normalization for RNA-Seq data
Covariate Assisted Large-scale Multiple testing
Covariate Assisted Large-scale Multiple testing
CPOP
CPOP
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
Create rapid visualizations of RNAseq data in R
Create rapid visualizations of RNAseq data in R
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)
Creation and Analysis of Pathway Expression Profiles (PEPs)
Cross-platform consensus analysis of genomic measurements via interlaboratory testing method
Cross-platform consensus analysis of genomic measurements via interlaboratory testing method
Cross Platform Meta-Analysis of Microarray Data
Cross Platform Meta-Analysis of Microarray Data
Data-Adaptive Statistics for High-Dimensional Multiple Testing
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 query/retrieval of species specific MSigDB versions
Decomposing Heterogeneous Cohorts using Omic Data Profiling
Decomposing Heterogeneous Cohorts using Omic Data Profiling
Deconvolution by Convex Analysis of Mixtures
Deconvolution by Convex Analysis of Mixtures
DegNorm: degradation normalization for RNA-seq data
Delineate outstanding genomic zones of differential gene activity
Delineate outstanding genomic zones of differential gene activity
DeMAND
Denoising Algorithm based on Relevance network Topology
DESeq2 Analysis Utilities
DESeq2 Analysis Utilities
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
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 hidden batch factors through data adaptive adjustment for biological effects
Detecting hidden batch factors through data adaptive adjustment for biological effects
Detecting hidden batch factors through data adaptive adjustment for biological effects
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 cell-cell interaction from single-cell RNA-seq dataset by tensor decomposition
Detect tissue heterogeneity in expression profiles with gene sets
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 Co-expression Analysis
Differential Co-expression Analysis
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 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 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
Different methods for the integrative analysis multiple omics data
Diffusion scores on biological networks
Diffusion scores on biological networks
Diffusion scores on biological networks
Dispersion shrinkage for sequencing data
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
doseR
doseR
doseR
doseR
Dry lab for exploring miRNA-mRNA relationships
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
EasyqpcR for low-throughput real-time quantitative PCR data analysis
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 Bayes estimate of block diagonal covariance matrices
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
Epigenomic tools
Epigenomic tools
EpiMethEx Package
Estimation of genetic and molecular regulatory networks from high-throughput genomics data
Estimation of genetic and molecular regulatory networks from high-throughput genomics data
Evaluate Cellspecific Mixing
Evaluate Cellspecific Mixing
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
Exon-Intron Split Analysis (EISA) in R
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 data analysis via the Iterative Signature Algorithm
Expression Weighted Celltype Enrichment
Expression Weighted Celltype Enrichment
Extraction of Differential Gene Expression
Extraction of Differential Gene Expression
Extraction of Differential Gene Expression
Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data
Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data
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 Correlation Based Filter for Feature Selection
Fast Gene Set Enrichment Analysis
Fast Gene Set Enrichment Analysis
Fast Permutation-based Gene Set Analysis
Fast Permutation-based Gene Set Analysis
Fast, Sensitive, and Accurate Integration of Single Cell Data
FCBF-based Co-Expression Networks for Single Cells
FCBF-based Co-Expression Networks for Single Cells
FCBF-based Co-Expression Networks for Single Cells
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
Find the most characteristic gene ontology terms for groups of human genes
Find the most characteristic gene ontology terms for groups of human genes
Find the most characteristic gene ontology terms for groups of human genes
Fishpond: differential transcript and gene expression with inferential replicates
Fishpond: differential transcript and gene expression with inferential replicates
Fit transcriptional regulatory networks using gene expression, priors, machine learning
Fit transcriptional regulatory networks using gene expression, priors, machine learning
Fit transcriptional regulatory networks using gene expression, priors, machine learning
Fit transcriptional regulatory networks using gene expression, priors, machine learning
Fit transcriptional regulatory networks using gene expression, priors, machine learning
For Visualizing Differential Expression Analysis
Functional interpretation of single cell RNA-seq latent manifolds
Functional interpretation of single cell RNA-seq latent manifolds
Functionality to Read and Manipulate SomaLogic ADAT files
Functionality to Read and Manipulate SomaLogic ADAT files
Functional Network Analysis
Functional Network Analysis
Functional similarities
Functional similarities
functions for genome-wide application of Liquid Association
functions for genome-wide application of Liquid Association
Functions for normalisation of RT-qPCR data
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
Functions useful for those doing repetitive analyses with Affymetrix GeneChips
GAPGOM (novel Gene Annotation Prediction and other GO Metrics)
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
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
GEM: fast association study for the interplay of Gene, Environment and Methylation
GEM: fast association study for the interplay of Gene, Environment and Methylation
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 changes in three biological conditions
Gene expression changes in three biological conditions
Gene expression enrichment in human brain regions
Gene expression enrichment in human brain regions
Gene Expression Meta-analysis Visualization Tool
Gene Expression Meta-analysis Visualization Tool
Gene Expression Signature based Similarity Metric
Gene Expression Signature based Similarity Metric
GEne Network Inference with Ensemble of trees
GEne Network Inference with Ensemble of trees
Gene Ontology analyser for RNA-seq and other length biased data
Gene Ontology analyser for RNA-seq and other length biased data
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
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
Generating Tree Hierarchy Visualizations from Gene Expression Data
Gene regulator enrichment analysis
Gene Regulatory Network Inference Using Time Series
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 (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 data structures and methods
Gene set enrichment data structures and methods
Gene Set Regulation (GS-Reg)
Gene Set Regulation (GS-Reg)
Gene Set Regulation (GS-Reg)
Genomic trajectories with heterogeneous genetic and environmental backgrounds
Genotype Imputed Gene Set Enrichment Analysis
Genotype Imputed Gene Set Enrichment Analysis
Global Test for Counts
Global Test for Counts
goProfiles: an R package for the statistical analysis of functional profiles
goProfiles: an R package for the statistical analysis of functional profiles
GPA (Genetic analysis incorporating Pleiotropy and Annotation)
GPA (Genetic analysis incorporating Pleiotropy and Annotation)
graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
GSCA: Gene Set Context Analysis
GSCA: Gene Set Context Analysis
GSCA: Gene Set Context Analysis
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
Hi-C Annotation and Graphics Ensemble
High-Throughput Sequence Analysis using the Aroma Framework
HiPathia: High-throughput Pathway Analysis
HiPathia: High-throughput Pathway Analysis
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 interaction networks and modules
Identification and analysis of miRNA sponge interaction networks and modules
Identification and analysis of miRNA sponge interaction networks and modules
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 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 genes associated with multiple expression phenotypes in single-cell CRISPR screening 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
Identifying Genes Overexpressed in Subsets of Tumors from Tumor-Normal mRNA Expression Data
Identify likely duplicate samples from genomic or meta-data
Identify likely duplicate samples from genomic or meta-data
Identify likely duplicate samples from genomic or meta-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
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
Import and summarize transcript-level estimates for transcript- and gene-level analysis
Improving replicability in single-cell RNA-Seq cell type discovery
Improving replicability in single-cell RNA-Seq cell type discovery
Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure
Inference of differential exon usage in RNA-Seq
Inference of differential exon usage in RNA-Seq
Inference of Genetic Variants Driving Cellular Phenotypes
Inferring miRNA sponge modules by integrating expression data and miRNA-target binding information
Inferring miRNA sponge modules by integrating expression data and miRNA-target binding information
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
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
In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data
integrated Bayesian Modeling of eQTL data
integrated Bayesian Modeling of eQTL data
Integrating Cap Enrichment with Transcript Expression Analysis
Integrating Cap Enrichment with Transcript Expression Analysis
Integrative analysis of Multi-omics data for Alternative Splicing
Integrative analysis of Multi-omics data for Alternative Splicing
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
Integrative Statistics of alleLe Dependent Expression
Interactive 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 Multi-Omics Cancers Data Visualization and Analysis
Interactive Multi-Omics Cancers Data Visualization and Analysis
Interactive SummarizedExperiment Explorer
Interactive SummarizedExperiment Explorer
Interactive SummarizedExperiment Explorer
Interactive SummarizedExperiment Explorer
Interactive visualization of scRNA-seq data with Cerebro
Interpretable marker-based single-cell pseudotime using Bayesian parametric models
Interpretable marker-based single-cell pseudotime using Bayesian parametric models
iSEE Universe
iSEE Universe
iSEE Universe
Judging Quality of Clustering Methods using Mutual Information
Judging Quality of Clustering Methods using Mutual Information
KMPPc: K-M Plot for Pan-cancer
KnowSeq R/Bioc package: Beyond the traditional Transcriptomic pipeline
KnowSeq R/Bioc package: Beyond the traditional Transcriptomic pipeline
Landscape Expression Visualization Interface
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
Learn and Apply Cell Type Signatures
Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level
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
Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs
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
LPEseq: local-pooled-error test for RNA-seq data with a small number of replicates
MAGMA.Celltyping
Make read coverage plots from BigWig files
Make read coverage plots from BigWig files
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
massiR: MicroArray Sample Sex Identifier
massiR: MicroArray Sample Sex Identifier
massiR: MicroArray Sample Sex Identifier
Massive and Integrative Gene Set Analysis
Massive and Integrative Gene Set Analysis
Massive correlating biclusters for gene expression data and associated methods
Massive correlating biclusters for gene expression data and associated methods
Massive correlating biclusters for gene expression data and associated methods
Maximum Likelihood Decay Modeling of RNA Degradation Data
Maximum Likelihood Decay Modeling of RNA Degradation Data
MetaAnalysis for High Throughput Experiments
MetaAnalysis for High Throughput Experiments
Meta-analysis of high-throughput experiments using feature annotations
Meta-analysis of high-throughput experiments using feature annotations
Meta-analysis of high-throughput experiments using feature annotations
Methods for Single-Cell RNA-Seq Data Analysis
Methods for Single-Cell RNA-Seq Data Analysis
Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape
Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape
Methylation array and sequencing spatial analysis methods
Methylation array and sequencing spatial analysis methods
Methylation array and sequencing spatial analysis methods
MethylMix: Identifying methylation driven cancer genes
MethylMix: Identifying methylation driven cancer genes
MethylMix: Identifying methylation driven cancer genes
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
Microbial Assemblage Normalized Transcript Analysis
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
Mini-batch K-means Clustering for Single-Cell RNA-seq
MiRNA Ranking by Gene Expression
Mixture Nested Effects Models
Mixture Nested Effects Models
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 higher-order methylation profiles
Model higher-order methylation profiles
Model higher-order methylation profiles
Modeling networks for individual samples using LIONESS
Modeling Network State Transitions from Expression and Regulatory data (MONSTER)
Modeling Network State Transitions from Expression and Regulatory data (MONSTER)
Monte Carlo Reference-based Consensus Clustering
Monte Carlo Reference-based Consensus Clustering
multiClust: An R-package for Identifying Biologically Relevant Clusters in Cancer Transcriptome Profiles
multiClust: An R-package for Identifying Biologically Relevant Clusters in Cancer Transcriptome Profiles
Multi-Contrast Gene Set Enrichment Analysis
Multi-Contrast Gene Set Enrichment Analysis
Multi-Contrast Gene Set Enrichment Analysis
Multiomic Batch effect Correction
Multiple Beta t-Tests
Multiple Beta t-Tests
Multiple omics data integrative clustering and gene set analysis
Multiple omics data integrative clustering and gene set analysis
Multiple Testing using SAM and Efron's Empirical Bayes Approaches
Multivariate Analysis of Transcriptomic Data
Multivariate Analysis of Transcriptomic Data
Multivariate Analysis of Transcriptomic Data
Multivariate Analysis of Transcriptomic Data
NanoString data normalization and differential gene expression analysis
Negative Binomial Additive Model for RNA-Seq Data
Negative Binomial Additive Model for RNA-Seq Data
Neighbor_net analysis
Network Perturbation Amplitude
Network Perturbation Amplitude
Network smoothing for scRNAseq
Network smoothing for scRNAseq
Non-detects in qPCR data
Non-detects in qPCR data
Non-detects in qPCR data
Obtain Raw Read Counts from RNASeq Data
Obtain Raw Read Counts from RNASeq Data
Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq
Outlier Analysis for pairwise differential comparison
Outlier Analysis for pairwise differential comparison
Outlier Analysis for pairwise differential comparison
Outlier Gene Set Analysis
outlier methods with applications in cancer
Outlier profile and pathway analysis in R
Outlier profile and pathway analysis in R
Outlier Protein and Phosphosite Target Identifier
Outlier Protein and Phosphosite Target Identifier
OUTRIDER - OUTlier in RNA-Seq fInDER
OUTRIDER - OUTlier in RNA-Seq fInDER
Overlay omics data onto SBGN pathway diagram
Overlay omics data onto SBGN pathway diagram
Overlay omics data onto SBGN pathway diagram
OVESEG-test to detect tissue/cell-specific markers
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 for Fold-specific GO Terms Recognition
Package for Fold-specific GO Terms Recognition
Package to work with miRNAs and miRNA targets with R
Pairwise INTegration of functional genomics data
Pairwise INTegration of functional genomics data
PANDA Algorithm
PANDA Algorithm
PANDA Algorithm
PANDA Algorithm
PatchseqMap
Pathway Enrichment Analysis Based on Bayesian Network
Pathway Enrichment Analysis Based on Bayesian Network
Pathway fingerprinting for analysis of gene expression arrays
Pathway fingerprinting for analysis of gene expression arrays
Pathway RespOnsive GENes for activity inference from gene expression
Pathway RespOnsive GENes for activity inference from gene expression
pcaGoPromoter is used to analyze DNA micro array data
PCAtools: Everything Principal Components Analysis
PCAtools: Everything Principal Components Analysis
Performance Assessment and Comparison for Survival Analysis
Performance Assessment and Comparison for Survival Analysis
Permutation-Based Confidence for Molecular Classification
pinnacle: Gene set enrichment analysis based on genomic intervals
pipeComp pipeline benchmarking framework
Pipeline for augmented co-expression analysis
pipeline for single cell RNA-seq data analysis
pipeline for single cell RNA-seq data analysis
Platform for integrative analysis of omics data
Platform for integrative analysis of omics data
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
PoTRA: Pathways of Topological Rank Analysis
PoTRA: Pathways of Topological Rank Analysis
Predict genes expressed selectively in specific cell types
Predict genes expressed selectively in specific cell types
Predicting Targets for Drosophila Intragenic miRNAs
Predicting Targets for Drosophila Intragenic miRNAs
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
Prize: an R package for prioritization estimation based on analytic hierarchy process
PRObabilistic Pathway Score (PROPS)
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
Profile RA-Seq Data Using TB Pathway Signatures
Profile RA-Seq Data Using TB Pathway Signatures
Profile RA-Seq Data Using TB Pathway Signatures
Projection onto Orthogonal Space Testing for High Dimensional Data
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
PROMISE analysis with Canonical Correlation for Two Forms of High Dimensional Genetic Data
Promoter identification from large-scale TSS profiling 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
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
Quality assessment and control for FFPE microarray expression data
Quality Control for Single-Cell RNA-seq Data
Quality Control for Single-Cell RNA-seq Data
Quality Control for Single-Cell RNA-seq Data
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-based single-sample gene set scoring method
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-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
R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts
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
rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines
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
Read qPCR data
Reconstruction, visualization and analysis of branching trajectories
Reconstruction, visualization and analysis of branching trajectories
Reconstruction, visualization and analysis of branching trajectories
Reference-Based Single-Cell RNA-Seq Annotation
Reference-Based Single-Cell RNA-Seq Annotation
Reference Index for Cell Types
Regression-based network inference using Bayesian Model Averaging
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
regutools: an R package for data extraction from RegulonDB
Removal of unwanted variation for gene-gene correlations and related analysis
Report of DEG analysis
Report of DEG analysis
Representing Different Biological Sets
Representing Different Biological Sets
Representing Different Biological Sets
Representing Different Biological Sets
Reproducibility-Optimized Test Statistic
Reproducible GSEA Benchmarking
Reproducible GSEA Benchmarking
R functions for the normalization of Exiqon miRNA array 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
RNAseq and qPCR signal comparison
RNA-Seq multi-mapping Reads Quantification Tool
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
R package for RIVER (RNA-Informed Variant Effect on Regulation)
R package for RIVER (RNA-Informed Variant Effect on Regulation)
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
RPA: Robust Probabilistic Averaging for probe-level analysis
rRice package to make easier the study of the genomic of rice
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
samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulation
samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulation
Sample Classifier
Sample Classifier
Sample Size Calculation for RNA-Seq Experimental Design
Sample Size Calculation for RNA-Seq Experimental Design
scClassify: single-cell Hierarchical Classification
scClassify: single-cell Hierarchical Classification
scDataviz: single cell dataviz and downstream analyses
scDataviz: single cell dataviz and downstream analyses
scMerge: Merging multiple batches of scRNA-seq data
scMerge: Merging multiple batches of scRNA-seq data
scRecover for imputation of single-cell RNA-seq data
scRecover for imputation of single-cell RNA-seq data
scRecover for imputation of single-cell RNA-seq data
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
Search for correlation between epigenetic signals and gene expression in TADs
Search for correlation between epigenetic signals and gene expression in TADs
Semi-parametric simulation tool for bulk and single-cell RNA sequencing data
Semi-supervised adaptive-height snipping of the Hierarchical Clustering tree
SEPA
SEPA
SEtools: tools for working with SummarizedExperiment
SEtools: tools for working with SummarizedExperiment
sigFeature: Significant feature selection using SVM-RFE & t-statistic
sigFeature: Significant feature selection using SVM-RFE & t-statistic
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 Prognostic Signatures
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
Simple Simulation of Single-cell RNA Sequencing Data
Simple Simulation of Single-cell RNA Sequencing Data
Simple Simulation of Single-cell RNA Sequencing Data
Simplified RNA-Seq Analysis Pipeline
Single-cell analysis toolkit for gene expression data in R
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 Batch Correction Methods
single-cell higher order testing
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 Overview of Normalized Expression data
Single cell replicability analysis
Single cell replicability analysis
Single-cell RNA-seq toolkit
Single-cell RNA-seq toolkit
Single-Cell RNA-Seq Utilities
Single-Cell RNA-Seq Utilities
Single Cell Shiny Application for Analysing Single Cell Transcriptomics Data
Single-cell Targetted Network Inference
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-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 Contrastive Principal Component Analysis
Sparse Partial Correlations On Gene Expression
Sparse Partial Correlations On Gene Expression
Sparse Partial Correlations On Gene Expression
Spatial Transcriptomics Analysis
Spatial Transcriptomics Analysis
SPIA-PCC: Signaling pathway impact analysis incorporated the change of Pearson correla-tion coefficient between two groups
Splice Interpreter of Transcripts
Splice Interpreter of Transcripts
ssPATHS: Single Sample PATHway Score
ssPATHS: Single Sample PATHway Score
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)
Statistics for Integrative Genomics Analyses in R
Strength of Selected Codon Usage
Subread Sequence Alignment and Counting for R
Subsampling of high-throughput sequencing 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
Summarization and expression/phenotype association of CNV ranges
Supervised Normalization of Microarrays
Supervised Normalization of Microarrays
supraHex: a supra-hexagonal map for analysing tabular omics data
supraHex: a supra-hexagonal map for analysing tabular omics data
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
Switch-like differential expression across single-cell trajectories
Synthetic Expression Data for Gene Regulatory Network Inference
systemPipeRdata: NGS workflow templates and sample data
systemPipeR: NGS workflow and report generation environment
systemPipeR: NGS workflow and report generation environment
Systems biology tool to simulate gene regulatory circuits
Systems biology tool to simulate gene regulatory circuits
Systems biology tool to simulate gene regulatory circuits
Systems biology tool to simulate gene regulatory circuits
Systems EPigenomics Inference of Regulatory Activity
Systems EPigenomics Inference of Regulatory Activity
Targeted Learning with Moderated Statistics for Biomarker Discovery
Targeted Learning with Moderated Statistics for Biomarker Discovery
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"
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 Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines
Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines
Tissue-specific gene enrichment analysis
Tissue-specific gene enrichment analysis
TNBC.CMS: Prediction of TNBC Consensus Molecular Subtypes
TNBC.CMS: Prediction of TNBC Consensus Molecular Subtypes
Tool for Evaluation of Cell Identity from Transcription Profiles
Tool for Evaluation of Cell Identity from Transcription Profiles
Toolkit for the automatic analysis of omics data
Toolkit for the automatic analysis of omics data
Tools for computational epigenomics
Tools for computational epigenomics
Tools for manipulating GO and microarrays
Tools for manipulating GO and microarrays
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 Efficient Analysis of High-Resolution Genomics Data
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
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
Transcriptional Data Guided fMRI Network Classification
Transcriptional Regulatory Inference from Genetics of Gene ExpRession
Transcriptional Regulatory Inference from Genetics of Gene ExpRession
Transcription factor Inference through Gaussian process Reconstruction of Expression
Transcription factor Inference through Gaussian process Reconstruction of Expression
Transcriptome instability analysis
Transcriptomic Ovarian Cancer Datasets
Transcriptomic Ovarian Cancer Datasets
Transcript Quantification Import with Automatic Metadata
Transcript Quantification Import with Automatic Metadata
Translational control assessment from ribosome footprint and total RNA libraries
TSCAN: Tools for Single-Cell ANalysis
TSCAN: Tools for Single-Cell ANalysis
Tumor subclonality of expression-based cancer subtypes
Turn Bioconductor objects into tidy data frames
Turn Bioconductor objects into tidy data frames
Unbiased Extraction of Single Cell Identity using Multiple Correspondence Analysis
Unbiased Extraction of Single Cell Identity using Multiple Correspondence Analysis
Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data
Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data
Unsupervised Identification of Genes with Expression Loss in Subsets of Tumors
Unsupervised Identification of Genes with Expression Loss in Subsets of Tumors
User Friendly Single-Cell and Bulk RNA Sequencing Visualization
User Friendly Single-Cell and Bulk RNA Sequencing Visualization
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
Utilities for Handling Single-Cell Droplet Data
Variance Adaptive Shrinkage
Varying-Censoring Aware Matrix Factorization
VirtUaL ChIP-Seq data Analysis using Networks
VirtUaL ChIP-Seq data Analysis using Networks
Virtual Inference of Protein-activity by Enriched Regulon analysis
Virtual Inference of Protein-activity by Enriched Regulon analysis
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 correlation results and test significancies of these
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
Visualize all edges within a KEGG pathway and overlay LINCS 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
Wavelet-Based Models for Tiling Array Transcriptome Analysis
Weighted matrix manipulation, finding components of variation with weighted or sparse data
Weighted matrix manipulation, finding components of variation with weighted or sparse data
What the Package Does (One Line, Title Case)
What the Package Does (One Line, Title Case)
What the Package Does TODOELI
Word cloud summaries of GO enrichment analysis
Word cloud summaries of GO enrichment analysis
YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization
YARN: Robust Multi-Condition RNA-Seq Preprocessing and Normalization
Zero-Inflated Negative Binomial Model for RNA-Seq Data
Zero-Inflated Negative Binomial Model for RNA-Seq Data