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
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 bioconductor package for exploration of alignment gap positions from RNA-seq 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
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
Add-on to DESeq to improve p-values and q-values
Affected pathway ranking in differential gene expression analysis
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.
A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC.
Agreement of Differential Expression Analysis
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
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
alpine
alpine
alpine
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
Analysis of alternative splicing using RNA-Seq
Analysis of alternative splicing using RNA-Seq
Analysis of alternative splicing using RNA-Seq
Analysis of alternative splicing using RNA-Seq
Analysis of amplicon enrichment panels
Analysis of amplicon enrichment panels
Analysis of 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 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 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 Translational Activity (ANOTA).
ANalysis Of Translational Activity (ANOTA).
Analyze and correct probe positional bias in microarray data due to RNA degradation
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
A new tool for exporting TCGA Firehose data
An integrated analysis package of Gene expression and Copy number alteration
An integrated analysis package of Gene expression and Copy number alteration
An integrated analysis package of miRNA and mRNA expression data
An integrated analysis package of miRNA and mRNA expression data
An integrated analysis package of miRNA and mRNA expression data
Annotation and gene expression data retrieval from Bgee database
Annotation and gene expression data retrieval from Bgee database
Annotation and gene expression data retrieval from Bgee database
annotation of noncoding RNAs and coexpressed genes
An R package for analyzing gene expression data with Principal / Independent Component Analysis
An R package for detecting chromatin state switches
An R package for qualitative biclustering in support of gene co-expression analyses
An R package for qualitative biclustering in support of gene co-expression analyses
An R package for 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 for the creation of complex genomic profile plots
An R package for the creation of complex genomic profile plots
An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
An R package to Identify, Annoatate and Visialize Isoform Switches with Functional Consequences (from RNA-seq data)
A package for survival time prediction based on a piecewise baseline hazard Cox regression model.
A package for survival time prediction based on a piecewise baseline hazard Cox regression model.
Application of gene classifiers
Application of gene classifiers
Application of gene classifiers
Approximate posterior estimation for GLM coefficients
Artificial Components Detection of Differentially Expressed Genes
Artificial Components Detection of Differentially Expressed Genes
Assess Differential Gene Expression Experiments with ERCC Controls
Assess Differential Gene Expression Experiments with ERCC Controls
Assess Differential Gene Expression Experiments with ERCC Controls
Assess Differential Gene Expression Experiments with ERCC Controls
Assign Properties to TNBC Patients
Assign Properties to TNBC Patients
Assign Properties to TNBC Patients
A suite of functions to facilitate zFPKM transformations
A suite of functions to facilitate zFPKM transformations
A Systems Biology Approach for Drug Repurposing
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 tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
a tool set for pathway based data integration and visualization
A tool to use GO Subtrees to Tag and Annotate Genes within a set
A tool to use GO Subtrees to Tag and Annotate Genes within a set
A tool to use GO Subtrees to Tag and Annotate Genes within a set
AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)
Automated analysis of high-throughput qPCR data
Automated analysis of high-throughput qPCR data
A web interface for gene-set enrichment analyses
A web interface for gene-set enrichment analyses
A work flow for analysis and normalization of pre-processing RT-qPCR data
Base Functions for Bioinformatics
Base Functions for Bioinformatics
Base Functions for Bioinformatics
Base Functions for Bioinformatics
Base package for enabling powerful shiny web displays of Bioconductor objects
Base package for enabling powerful shiny web displays of Bioconductor objects
Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments
Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments
Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments
Bayesian hierarchical mixture of factor analyzers for modelling genomic bifurcations
Bayesian Inference of Regulation of Transcriptional Activity
Bayesian Inference of Regulation of Transcriptional Activity
Bayesian Inference of Regulatory Influence on Expression (biRte)
Bayesian Inference of Regulatory Influence on Expression (biRte)
BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data
BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data
BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data
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
Better prediction by use of co-data: Adaptive group-regularized ridge regression
BIMEGA: BIvariate Methylation and Expression GAussian mixture model
Calculates Mulcom test
Calculates Mulcom test
Cancer subtypes identification, validation and visualization based on genomic data
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
Candidate gene prioritization based on convergent evidence
Cell OrderiNg by FluorEScence Signal
Cell OrderiNg by FluorEScence Signal
Characterization of Alternative Splicing based on Paired-End Reads
Characterization of Alternative Splicing based on Paired-End Reads
Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata
Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata
Chromosmal Aberrations Finder in Expression data
Chromosmal Aberrations Finder in Expression data
Classification of alternative splicing and prediction of coding potential from RNA-seq data.
Classification of alternative splicing and prediction of coding potential from RNA-seq data.
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 and Visualizing RNA-Seq Expression Data using Grade of Membership Models
Clustering approach to solve complete Deconvolution problem
Clustering Comparison Package
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, differential expression, and trajectory analysis for single- cell RNA-Seq
Clustering of high-throughput sequencing data by identifying co-expression patterns
Clustering of high-throughput sequencing data by identifying co-expression patterns
Clustering of high-throughput sequencing data by identifying co-expression patterns
Clustering of Time Series Gene Expression data
Clustering of Time Series Gene Expression data
Clustering of Time Series Gene Expression data
coexnet: An R package to build CO-EXpression NETworks from Microarray Data
coexnet: An R package to build CO-EXpression NETworks from Microarray Data
coexnet: An R package to build CO-EXpression NETworks from Microarray Data
co-expressed gene-set enrichment analysis
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
Co-Expression Analysis of Sequencing Data
Co-Expression Modules identification Tool
co-expression of lincRNAs and protein-coding genes
co-expression of lincRNAs and protein-coding genes
co-expression of lincRNAs and protein-coding genes
Combination Connectivity Mapping
Combination Connectivity Mapping
Combination Connectivity Mapping
Comparison between multiple levels of gene expression
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 transciptome 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
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
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
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.
Coordinated Gene Activity in Pattern Sets
Coordinated Gene Activity in Pattern Sets
Coordinated Gene Activity in Pattern Sets
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
CoRegNet : reconstruction and integrated analysis of co-regulatory networks
Count summarization and normalization for RNA-Seq data
Count summarization and normalization for RNA-Seq data
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
Cross Platform Meta-Analysis of Microarray Data
Cross Platform Meta-Analysis of Microarray Data
Cross Platform Meta-Analysis of Microarray Data
Data-driven normalization strategies for high-throughput qPCR data.
Data-driven normalization strategies for high-throughput qPCR data.
Data for the alpine package vignette
debrowser: Interactive Differential Expresion Analysis Browser
debrowser: Interactive Differential Expresion Analysis Browser
debrowser: Interactive Differential Expresion Analysis Browser
DeMAND
DeMAND
Denoising Algorithm based on Relevance network Topology
Denoising Algorithm based on Relevance network Topology
Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm
Design gene based on both mRNA secondary structure and codon usage bias using Genetic algorithm
DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments
DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments
DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments
Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM)
Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM)
Detecting hidden batch factors through data adaptive adjustment for biological effects
Detecting hidden batch factors through data adaptive adjustment for biological effects
Detect tissue heterogeneity in expression profiles with gene sets
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
DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates
Differential expression analysis of longitudinal count data sets
Differential expression analysis of longitudinal count data sets
Differential expression analysis of longitudinal count data sets
Differential gene expression analysis based on the negative binomial distribution
Differential gene expression analysis based on the negative binomial distribution
Differential gene expression analysis based on the negative binomial distribution
Differential gene expression data formats converter
Differential gene expression data formats converter
Differential gene expression data formats converter
Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
Diffusion scores on biological networks
Diffusion scores on biological networks
Diffusion scores on biological networks
Dispersion shrinakge for sequencing data.
Dispersion shrinkage for sequencing data.
Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles
Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles
Dry lab for exploring miRNA-mRNA relationships
Dry lab for exploring miRNA-mRNA relationships
Dynamic Transcriptome Analysis
Dynamic Transcriptome Analysis
Earth Mover's Distance for Differential Analysis of Genomics Data
Earth Mover's Distance for Differential Analysis of Genomics Data
Earth Mover's Distance for Differential Analysis of Genomics Data
Easy Analysis of RNASeq DE
Easy Analysis of RNASeq DE
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
ELBOW - Evaluating foLd change By the lOgit Way
Empirical Analysis of Digital Gene Expression Data in R
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 Bayes estimate of block diagonal covariance matrices
Engineering Evaluation by Gene Categorization (eegc)
Engineering Evaluation by Gene Categorization (eegc)
Engineering Evaluation by Gene Categorization (eegc)
Ensemble of Gene Set Enrichment Analyses
Ensemble of Gene Set Enrichment Analyses
Epigenetic and gene transcription data normalization and integration with mixture models
Epigenetic and gene transcription data normalization and integration with mixture models
Epigenomic tools
Epigenomic tools
Estimation of genetic and molecular regulatory networks from high-throughput genomics data
Estimation of genetic and molecular regulatory networks from high-throughput genomics data
Exon Based Strategy for Expression Analysis of genes
Exon Based Strategy for Expression Analysis of genes
Explore and download data from the recount project
Explore and download data from the recount project
Explore and download data from the recount project
Exposome and omic data associatin and integration analysis
Expression data analysis via the Iterative Signature Algorithm
Expression data analysis via the Iterative Signature Algorithm
Expression Weighted Celltype Enrichment
Expression Weighted Celltype Enrichment
Extended project Morpheus with Bioconductor methods
Extended project Morpheus with Bioconductor methods
Extraction of Differential Gene Expression
Extraction of Differential Gene Expression
Extraction of Differential Gene Expression
Extraction of Differential Gene Expression
Factor Loading Adaptive SHrinkage in R
FARMS - Factor Analysis for Robust Microarray Summarization
FARMS - Factor Analysis for Robust Microarray Summarization
Fast Gene Set Enrichment Analysis
Fast Gene Set Enrichment Analysis
Fast Gene Set Enrichment Analysis
Fast Permutation-based Gene Set Analysis
Fast Permutation-based Gene Set Analysis
Fast Permutation-based Gene Set Analysis
Filter replicated high-throughput transcriptome sequencing data
Filter replicated high-throughput transcriptome sequencing data
Finds Gene Co-expression Modules
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
Find the most characteristic gene ontology terms for groups of human genes
Fit transcriptional regulatory networks using gene expression, priors, machine learning
Functionality to Read and Manipulate SomaLogic ADAT files
Functionality to Read and Manipulate SomaLogic ADAT files
Functionality to Read and Manipulate SomaLogic ADAT files
Functional Network Analysis
Functional Network Analysis
Functional Network Analysis
Functional similarities
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 useful for those doing repetitive analyses with Affymetrix GeneChips
Functions useful for those doing repetitive analyses with Affymetrix GeneChips
Functions useful for those doing repetitive analyses with Affymetrix GeneChips
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
GEM: fast association study for the interplay of Gene, Environment and Methylation
Gene Expression Atlas query and gene set enrichment package.
Gene Expression Atlas query and gene set enrichment package.
Gene expression-based subtype classification for high-grade serous ovarian cancer
Gene expression-based subtype classification for high-grade serous ovarian cancer
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 Signature based Similarity Metric
Gene Expression Signature based Similarity Metric
Gene Expression Signature based Similarity Metric
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 Gene-set Enrichment for Pathway Analysis
General Sample Size and Power Analysis for Microarray and Next-Generation Sequencing Data
General Sample Size and Power Analysis for Microarray and Next-Generation Sequencing Data
Gene Regulatory Network Inference Using Time Series
Gene Regulatory Network Inference Using Time Series
Gene Set Enrichment Analysis Extended to Contingency Cubes
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 data structures and methods
Gene set enrichment data structures and methods
Gene Set Regulation (GS-Reg)
Gene Set Regulation (GS-Reg)
goProfiles: an R package for the statistical analysis of functional profiles
goProfiles: an R package for the statistical analysis of functional profiles
GSCA: Gene Set Context Analysis
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 Affymetrix microarrays
GUI for limma package with two color microarrays
GUI for limma package with two color microarrays
High-Throughput Sequence Analysis using the Aroma Framework
Hybrid Multiple Testing
Hybrid Multiple Testing
Identification and analysis of miRNA sponge interaction networks and modules
Identification of genetic Variants affecting Alternative Splicing
Identification of genetic Variants affecting Alternative Splicing
Identify Differentially Expressed Genes from RNA-seq data
Identify Differentially Expressed Genes from RNA-seq data
Identify 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
Identify oncogenes and tumor suppressor genes from omics data
Illumina 450K methylation array spatial analysis methods
Implementation of gene expression anti-profiles
Implementation of gene expression anti-profiles
Import and summarize transcript-level estimates for gene-level analysis
Import and summarize transcript-level estimates for transcript- and gene-level analysis
Import and summarize transcript-level estimates for transcript- and gene-level analysis
Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure
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
Inference of Genetic Variants Driving Cellular Phenotypes
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
Infers biological signatures from gene expression data
Infers biological signatures from gene expression data
integrated Bayesian Modeling of eQTL data
integrated Bayesian Modeling of eQTL data
integrated Bayesian Modeling of eQTL data
Integrative analysis of Multi-omics data for Alternative Splicing
Integrative analysis of Multi-omics data for Alternative Splicing
Integrative analysis of Multi-omics data for Alternative Splicing
Integrative Statistics of alleLe Dependent Expression
Integrative Statistics of alleLe Dependent Expression
Interactive Differential Expression AnaLysis
Interactive Differential Expression AnaLysis
Interactive HTML graphics
Interactive HTML graphics
Interactive HTML graphics
Interactive Multi-Omics Cancers Data Visualization and Analysis
Interactive Multi-Omics Cancers Data Visualization and Analysis
Interactive Multi-Omics Cancers Data Visualization and Analysis
Interpretable marker-based single-cell pseudotime using Bayesian parametric models
Interpretable marker-based single-cell pseudotime using Bayesian parametric models
Judging Quality of Clustering Methods using Mutual Information
Judging Quality of Clustering Methods using Mutual Information
Laplacian eigenmaps & principal curves for pseudotemporal ordering of single-cell RNA-seq data
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
Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene, Pathway and Network Level
Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene, Pathway and Network Level
Linear model and normality based transformation method (Linnorm)
Linear model and normality based transformation method (Linnorm)
Linear Models for Microarray Data
Linear Models for Microarray Data
LiquidAssociation
LiquidAssociation
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
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 Microarray gene expression data
Marker Gene Finder in RNA-seq data
Marker Gene Finder in RNA-seq data
massiR: MicroArray Sample Sex Identifier
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 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
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
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 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
Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
Microarray Analysis of Differential Expression
Microbial Assemblage Normalized Transcript Analysis
Microbial Assemblage Normalized Transcript Analysis
MiRNA Ranking by Gene Expression
MiRNA Ranking by Gene Expression
MODA: MOdule Differential Analysis for weighted gene co-expression network
MODA: MOdule Differential Analysis for weighted gene co-expression network
MODA: MOdule Differential Analysis for weighted gene co-expression network
Model-based Analysis of Single Cell Transcriptomics
Model-based Analysis of Single Cell Transcriptomics
Model-based Analysis of Single Cell Transcriptomics
Model higher-order methylation profiles
Model higher-order methylation profiles
Model higher-order methylation profiles
Model higher-order methylation profiles
Modeling Network State Transitions from Expression and Regulatory data (MONSTER)
Modeling Network State Transitions from Expression and Regulatory data (MONSTER)
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
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
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
Non-detects in qPCR data
Non-detects in qPCR data
Non-detects in qPCR data
Obtain and visualize regulome (micorRNA/transcription factors)-gene correlations in cancer
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
Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq
Outlier Gene Set Analysis
Outlier Gene Set Analysis
Outlier profile and pathway analysis in R
Outlier profile and pathway analysis in R
Outlier profile and pathway analysis in R
Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection
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 enabling powerful shiny web displays of Bioconductor objects
Package for Topology-based Pathway Analysis of RNASeq data
Package for Topology-based Pathway Analysis of RNASeq data
Package to work with miRNAs and miRNA targets with R
Package to work with miRNAs and miRNA targets with R
Pairwise Integration of Functional Genomics Data
Pairwise INTegration of functional genomics data
Pairwise INTegration of functional genomics data
PANDA Algorithm
PANDA Algorithm
PANDA Algorithm
PANDA Algorithm
Pathway fingerprinting for analysis of gene expression arrays
Pathway fingerprinting for analysis of gene expression arrays
Pathway fingerprinting for analysis of gene expression arrays
pcaGoPromoter is used to analyze DNA micro array data
pcaGoPromoter is used to analyze DNA micro array data
Performance Assessment and Comparison for Survival Analysis
Performance Assessment and Comparison for Survival Analysis
Performance Assessment and Comparison for Survival Analysis
Permutation-Based Confidence for Molecular Classification
Permutation-Based Confidence for Molecular Classification
pipeline for single cell RNA-seq data analysis
Platform for integrative analysis of omics data
Platform for integrative analysis of omics data
Position Related Data Analysis
Position Related Data Analysis
Predict genes expressed selectively in specific cell types
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
Principal Coordinates and Hotelling's T-Square method
Prize: an R package for prioritization estimation based on analytic hierarchy process
Prize: an R package for prioritization estimation based on analytic hierarchy process
Probe-level Expression Change Averaging
Probe-level Expression Change Averaging
Probe region expression estimation for RNA-seq data for improved microarray comparability
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 and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays
Projection onto Orthogonal Space Testing for High Dimensional Data
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
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
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
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)
Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)
QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data
QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data
Quality assessment and control for FFPE microarray 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
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
Rank Product method for identifying differentially expressed genes with application in meta-analysis
Rank Product method for identifying differentially expressed genes with application in meta-analysis
R-based analysis of ChIP-seq And Differential Expression - a tool for integrating a count-based ChIP-seq analysis with differential expression summary data
R-based analysis of ChIP-seq And Differential Expression - a tool for integrating a count-based ChIP-seq analysis with differential expression summary data
RBioinf
RBioinf
rcellminer: Molecular Profiles and Drug Response for the NCI-60 Cell Lines
rcellminer: Molecular Profiles and Drug Response for the NCI-60 Cell Lines
rcellminer: Molecular Profiles and Drug Response for the NCI-60 Cell Lines
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
Read qPCR data
Read qPCR data
Reconstruction of transcriptional networks and analysis of master regulators
Reconstruction of transcriptional networks and analysis of master regulators
Regression-based network inference using Bayesian Model Averaging
Regression-based network inference using Bayesian Model Averaging
Removal of unwanted variation for gene-gene correlations and related analysis
Removal of unwanted variation for gene-gene correlations and related analysis
Report of DEG analysis
Report of DEG analysis
Report of DEG analysis
Reproducibility-Optimized Test Statistic
Reproducibility-Optimized Test Statistic
R functions for the normalization of Exiqon miRNA array data
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
RNAseq and qPCR signal comparison
RnaSeqSampleSize
RnaSeqSampleSize
rnaSeq secondary analyses
rnaSeq secondary analyses
RNA-Seq Utilities
RNA-Seq Utilities
R Normalization and Inference of Time Series data
R Normalization and Inference of Time Series data
R Normalization and Inference of Time Series data
Robust Probabilistic Averaging for probe-level analysis (RPA)
Routines for the functional analysis of biological networks
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 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 for the statistical assessment of cell state hierarchies from single-cell RNA-seq data
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
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
samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulation
Sample Classifier
Sample Classifier
Sample Classifier
Sample Size Calculation for RNA-Seq Experimental Design
Sample Size Calculation for RNA-Seq Experimental Design
Seamless navigation through combined results of set-based and network-based enrichment analysis
Seamless navigation through combined results of set-based and network-based enrichment analysis
Semi-supervised adaptive-height snipping of the Hierarchical Clustering tree
Semi-supervised adaptive-height snipping of the Hierarchical Clustering tree
SEPA
SEPA
SEPA
Sexual dimorphic and COPD differential analysis for gene expression and methylation.
signet: Selection Inference in Gene NETworks
Significance Analysis of Prognostic Signatures
Significance Analysis of Prognostic Signatures
Significance Analysis of Prognostic Signatures
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
Simplified RNA-Seq Analysis Pipeline
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 Overview of Normalized Expression data
Single Cell Overview of Normalized Expression data
Single Cell Overview of Normalized Expression data
Single-Cell RNA-Seq Utilities
Single-Cell RNA-Seq Utilities
Single-gene classifiers and outlier-resistant detection of differential expression for two-group and survival problems.
Single-gene classifiers and outlier-resistant detection of differential expression for two-group and survival problems.
small RNA-Seq Utilities
software and data for analyses in genetics of gene expression
software and data for analyses in genetics of gene expression
Splice Interpreter Of Transcripts
Splice Interpreter Of Transcripts
Statistical analysis of sequins
Statistical analysis of sequins
Statistical analysis of sequins
Statistical Analysis of the GeneChip
Statistical Analysis of the GeneChip
Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD)
Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD)
Statistics for Integrative Genomics Analyses in R
Statistics for Integrative Genomics Analyses in R
Strength of Selected Codon Usage
Strength of Selected Codon Usage
Subread sequence alignment for R
Subread sequence alignment for R
Subsampling of high-throughput sequencing count data
Subsampling of high-throughput sequencing count data
Subsampling of high-throughput sequencing count data
Supervised Normalization of Microarrays
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
supraHex: a supra-hexagonal map for analysing tabular omics data
SVAPLSseq-An R package to adjust for the hidden factors of variability in differential gene expression studies based on RNAseq data
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
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
Targeted Learning for Biomarker Discovery with Moderated Statistics
Targeted Learning for Biomarker Discovery with Moderated Statistics
Targeted Learning for Biomarker Discovery with Moderated Statistics
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data
"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"
"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"
"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"
Testing for association between RNA-Seq and high-dimensional data
Testing for association between RNA-Seq and high-dimensional data
Testing for association between RNA-Seq and high-dimensional data
The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)
The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)
Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction
Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction
Time-course differential gene expression data analysis using spline regression models followed by gene association network reconstruction
Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines
Title: SIMLR: Single-cell Interpretation via Multi-kernel LeaRning
Title: SIMLR: Single-cell Interpretation via Multi-kernel LeaRning
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
Transcript expression inference and differential expression analysis for RNA-seq data
Transcript expression inference and differential expression analysis for RNA-seq data
Transcriptional Regulatory Inference from Genetics of Gene ExpRession
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
Transcriptome instability analysis
TSCAN: Tools for Single-Cell ANalysis
TSCAN: Tools for Single-Cell ANalysis
TSCAN: Tools for Single-Cell ANalysis
Turn Bioconductor objects into tidy data frames
Turn Bioconductor objects into tidy data frames
Turn Bioconductor objects into tidy data frames
Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data
Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data
Uses Brown's method to combine p-values from dependent tests
Uses Brown's method to combine p-values from dependent tests
Variance Adaptive Shrinkage
Varying-Censoring Aware Matrix Factorization
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
Virtual Inference of Protein-activity by Enriched Regulon analysis
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualise microarray and RNAseq data using gene ontology annotations
Visualize all edges within a KEGG pathway and overlay LINCS data [option]
Visualize all edges within a KEGG pathway and overlay LINCS data [option]
Visualize all edges within a KEGG pathway and overlay LINCS data [option]
Visualize all edges within a KEGG pathway and overlay LINCS data [option]
Visualize biclusters identified in gene expression data
Visualize biclusters identified in gene expression data
Wavelet-Based Models for Tiling Array Transcriptome Analysis
Wavelet-Based Models for Tiling Array Transcriptome Analysis
Wavelet-Based Models for Tiling Array Transcriptome Analysis
Word cloud summaries of GO enrichment analysis
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
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