Biocview "RNASeq"

Add-on to DESeq to improve p-values and q-values
Add-on to DESeq to improve p-values and q-values
Adjust for positional and batch effects using ComBat
Adjust for positional and batch effects using ComBat
A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops
A graphical interface designed to facilitate analysis of microarrays and miRNA/RNA-seq data on laptops
AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype
AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype
AIPS : Absolute Inference of Patient Signatures
alpine
alpine
alpine
Analysis of 4sU-seq and RNA-seq time-course data
Analysis of 4sU-seq and RNA-seq time-course 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 Differential Abundance Taking Sample Variation Into Account
Analysis Of Differential Abundance Taking Sample Variation Into Account
Analysis of RNA-Seq Count Data by Using Multiple Corespondence Analysis
Analysis of RNA-Seq Count Data by Using Multiple Corespondence Analysis
Analyze isomiRs and miRNAs from small RNA-seq
Analyze isomiRs and miRNAs from small RNA-seq
Analyze isomiRs and miRNAs from small RNA-seq
An effective identification of alternative splicing events using junction arrays and RNA-Seq data
An effective identification of alternative splicing events using junction arrays and RNA-Seq data
An effective identification of alternative splicing events using junction arrays and RNA-Seq data
An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification
An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification
An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps
An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps
An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps
An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps.
Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
An package for identification of novel peptides by customized database derived from RNA-Seq
An package for identification of novel peptides by customized database derived from RNA-Seq
An R Package for Adjusting Bias in Gene Set Enrichment Analysis
An R Package for Adjusting Bias in Gene Set Enrichment Analysis
An R package for gene and isoform differential expression analysis of RNA-seq data
An R package for gene and isoform differential expression analysis of RNA-seq data
An R package for gene and isoform differential expression analysis of RNA-seq data
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 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 variant peptides detection and visualization in shotgun proteomics.
A package for variant peptides detection and visualization in shotgun proteomics.
Approximate posterior estimation for GLM coefficients
ArrayExpress High Throughput Sequencing Processing Pipeline
ArrayExpress High Throughput Sequencing Processing Pipeline
A Shiny App to accompany clusterExperiment
A small RNA-seq visualizer and analysis toolkit
A small RNA-seq visualizer and analysis toolkit
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
Assessment of duplication rates in RNA-Seq datasets
Assessment of duplication rates in RNA-Seq datasets
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 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 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
Base Functions for Bioinformatics
Base Functions for Bioinformatics
Base Functions for Bioinformatics
Base Functions for Bioinformatics
Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
Batch Effects Quality Control Software
Batch Effects Quality Control Software
Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments
Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments
Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments
Bayesian Analysis of Differential Expression in RNA Sequencing Data
Bayesian Analysis of Differential Expression in RNA Sequencing Data
Bayesian hierarchical mixture of factor analyzers for modelling genomic bifurcations
Benchmarks for RNA-seq Quantification Pipelines
Benchmarks for RNA-seq Quantification Pipelines
Benchmarks for RNA-seq Quantification Pipelines
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
Biostatistical Analysis Reporting Tool
Causal network analysis methods
Causal network analysis methods
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
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, 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 Time Series Gene Expression data
Clustering of Time Series Gene Expression data
Clustering of Time Series Gene Expression data
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
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns
coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns.
Compare Characteristic Features of Count Data Sets
Compare Clusterings for Single-Cell Sequencing
Compare Clusterings for Single-Cell Sequencing
Compare Clusterings for Single-Cell Sequencing
Compare Clusterings for Single-Cell Sequencing
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
Compute coverage matrices from recount quickly using bwtool
ComSeq: An ensemble method for RNA-Seq differential analysis
ComSeq: An ensemble method for RNA-Seq differential analysis
Conditional quantile normalization
Conditional quantile normalization
Controlling bias and inflation in association studies using the empirical null distribution
Controlling bias and inflation in association studies using the empirical null distribution
Coordinated Gene Activity in Pattern Sets
Coordinated Gene Activity in Pattern Sets
Coordinated Gene Activity in Pattern Sets
Count summarization and normalization for RNA-Seq data
Count summarization and normalization for RNA-Seq data
Coverage visualization package for R
Coverage visualization package for R
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them
Data for the alpine package vignette
Data Mining for RNA-seq data: normalization, feature selection and classification
Data Mining for RNA-seq data: normalization, feature selection and classification
Data Mining for RNA-seq data: normalization, feature selection and classification
debrowser: Interactive Differential Expresion Analysis Browser
debrowser: Interactive Differential Expresion Analysis Browser
debrowser: Interactive Differential Expresion Analysis Browser
derfinder helper package
derfinder helper package
derfinder helper package
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
Detecting hidden batch factors through data adaptive adjustment for biological effects
Detecting hidden batch factors through data adaptive adjustment for biological effects
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 gene expression analysis based on the negative binomial distribution
Differential gene expression analysis based on the negative binomial distribution
Differential gene expression analysis based on the negative binomial distribution
Differential gene expression analysis based on the negative binomial distribution
Differential gene expression analysis based on the negative binomial distribution
Differential gene expression data formats converter
Differential gene expression data formats converter
Differential gene 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
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
Easy Analysis of RNASeq DE
Easy Analysis of RNASeq DE
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
Empirical Method of Optimal Pvalue Weighting
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
Experimental Design in Differential Abundance analysis
Experimental Design in Differential Abundance analysis
Exploratory analysis and differential expression for RNA-seq data
Exploratory analysis and differential expression for RNA-seq data
Exploratory Data Analysis and Normalization for RNA-Seq
Exploratory Data Analysis and Normalization for RNA-Seq
Exploratory Data Analysis and Normalization for RNA-Seq
Explore and download data from the recount project
Explore and download data from the recount project
Explore and download data from the recount project
Expression Weighted Celltype Enrichment
Expression Weighted Celltype Enrichment
Factor Loading Adaptive SHrinkage in R
Fast lasso-based isoform prediction as a flow problem
Fast lasso-based isoform prediction as a flow problem
Fast Reading and Processing of Common Gene Annotation and Next Generation Sequencing Format Files
Fast Reading and Processing of Common Gene Annotation and Next Generation Sequencing Format Files
Filter replicated high-throughput transcriptome sequencing data
Filter replicated high-throughput transcriptome sequencing data
Finds Gene Co-expression Modules
Flexible, isoform-level differential expression analysis
Flexible, isoform-level differential expression analysis
Flexible, isoform-level differential expression analysis
Flexible, isoform-level differential expression analysis
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
Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search
Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Generate Summary Plots of FastQC Reports
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 / Projection Displays
Gene Set Enrichment / Projection Displays
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Guitar
Guitar
iASeq: integrating multiple sequencing datasets for detecting allele-specific events
iASeq: integrating multiple sequencing datasets for detecting allele-specific events
Identification of genetic Variants affecting Alternative Splicing
Identification of genetic Variants affecting Alternative Splicing
Identification of Novel alternative PolyAdenylation Sites (PAS)
Identification of Novel alternative PolyAdenylation Sites (PAS)
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
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
Independent Hypothesis Weighting
Independent Hypothesis Weighting
Independent Hypothesis Weighting
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
Infers biological signatures from gene expression data
Infers biological signatures from gene expression 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 Visualization of RNA-seq Data Using a Principal Components Approach
Interactive Visualization of RNA-seq Data Using a Principal Components Approach
Interactive Visualization of RNA-seq Data Using a Principal Components Approach
Interpretable marker-based single-cell pseudotime using Bayesian parametric models
Interpretable marker-based single-cell pseudotime using Bayesian parametric models
Intron-Exon Retention Estimator
Intron-Exon Retention Estimator
Intron-Exon Retention Estimator
Isoform expression estimation based on RNA-seq data
JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data
JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data
L1-regularization based methods for detection of differential splicing
L1-regularization based methods for detection of differential splicing
L1-regularization based methods for detection of differential splicing
Laplacian eigenmaps & principal curves for pseudotemporal ordering of single-cell RNA-seq data
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
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
Machine learning interface for RNA-Seq data
Machine learning interface for RNA-Seq data
Machine Learning Interface for RNA-Seq Data
Make read coverage plots from BigWig files
Make read coverage plots from BigWig files
Marker Gene Finder in RNA-seq data
Marker Gene Finder in RNA-seq data
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
Meta-analysis of RNA-Seq count data in multiple studies
Meta-analysis of RNA-Seq count data in multiple studies
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
Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape
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
Microbial Assemblage Normalized Transcript Analysis
Microbial Assemblage Normalized Transcript Analysis
MiRNA Ranking by Gene Expression
MiRNA Ranking by Gene Expression
Mixture modeling of single-cell RNA-seq data to indentify genes with differential distributions
Mixture modeling of single-cell RNA-seq data to indentify genes with differential distributions
Mixture modeling of single-cell RNA-seq data to indentify genes with differential distributions
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
Monte Carlo Consensus Clustering
Multivariate and directional gene set testing
Multivariate and directional gene set testing
Normalization of single cell RNA-seq data
Normalization of single cell RNA-seq data
Obtain Raw Read Counts from RNASeq Data
Obtain Raw Read Counts from RNASeq Data
Optimal p-value weighting with independent information
Optimal p-value weighting with independent information
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
Package for Topology-based Pathway Analysis of RNASeq data
Package for Topology-based Pathway Analysis of RNASeq data
Parallel implmentation of bounded memory GEE
PathoStat Statistical Microbiome Analysis Package
PathoStat Statistical Microbiome Analysis Package
PathoStat Statistical Microbiome Analysis Package
Permutation-Based Confidence for Molecular Classification
Permutation-Based Confidence for Molecular Classification
pipeline for single cell RNA-seq data analysis
Plots of Statistics Collected by Qualimap from RNASeq Data
Plotting functions for derfinder
Plotting functions for derfinder
Plotting functions for derfinder
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 region expression estimation for RNA-seq data for improved microarray comparability
Probe region expression estimation for RNA-seq data for improved microarray comparability
PROspective Power Evaluation for RNAseq
PROspective Power Evaluation for RNAseq
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 Annotate Short Reads in R
Quantify and Annotate Short Reads in R
Quantify and interpret divers of variation in multilevel gene expression experiments
Quantify and interpret divers of variation in multilevel gene expression experiments
qusage: Quantitative Set Analysis for Gene Expression
qusage: Quantitative Set Analysis for Gene Expression
qusage: Quantitative Set Analysis for Gene Expression
Rcpp Integration Surrogate Variable Analysis
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
Remove Unwanted Variation from RNA-Seq Data
Remove Unwanted Variation from RNA-Seq Data
Remove Unwanted Variation from RNA-Seq Data
Report of DEG analysis
Report of DEG analysis
Report of DEG analysis
Representation and manipulation of short genomic alignments
Representation and manipulation of short genomic alignments
Reproducibility-Optimized Test Statistic
Reproducibility-Optimized Test Statistic
RNA-seq data analysis using the Poisson-Tweedie family of distributions
RNA-seq data analysis using the Poisson-Tweedie family of distributions
RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods
RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods
RnaSeqSampleSize
RnaSeqSampleSize
rnaSeq secondary analyses
rnaSeq secondary analyses
RNA-Seq Utilities
RNA-Seq Utilities
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
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
Sample size for RNAseq studies
Sample size for RNAseq studies
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
Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data
Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data
Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size
Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size
SigFuge
SigFuge
SigFuge
Significance-based Modules Integrating the Transcriptome and Epigenome
Significance-based Modules Integrating the Transcriptome and Epigenome
Significance-based Modules Integrating the Transcriptome and Epigenome
Simple Simulation of Single-cell RNA Sequencing Data
Simple Simulation of Single-cell RNA Sequencing Data
Simple Simulation of Single-cell RNA Sequencing Data
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 Consensus Clustering
Single-Cell Consensus Clustering
Single-Cell Consensus Clustering
Single Cell Differential Expression
Single Cell Differential Expression
Single Cell Differential Expression
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-channel array normalization (SCAN) and Universal exPression Codes (UPC)
Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
Splice event prediction and quantification from RNA-seq data
Splice event prediction and quantification from RNA-seq data
Splice Interpreter Of Transcripts
Splice Interpreter Of Transcripts
Statistical analysis of sequins
Statistical analysis of sequins
Statistical analysis of sequins
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
Suite of Functions for Pooled Crispr Screen QC and Analysis
Suite of Functions for Pooled Crispr Screen QC and Analysis
Suite of Functions for Pooled Crispr Screen QC and Analysis
Surrogate Variable Analysis
Surrogate Variable Analysis
Surrogate Variable Analysis
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 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
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
TCC: Differential expression analysis for tag count data with robust normalization strategies
TCC: Differential expression analysis for tag count data with robust normalization strategies
Test for differential expression for RNA-seq data
Test for differential expression for RNA-seq 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 Cancer Genome Atlas Data Integration
The Cancer Genome Atlas Data Integration
The Cancer Genome Atlas Data Integration
The Discordant Method: A Novel Approach for Differential Correlation
The Discordant Method: A Novel Approach for Differential Correlation
The Discordant Method: A Novel Approach for Differential Correlation
The genomic STate ANnotation package
The Genomic STate ANnotation Package
Time course sequencing data analysis
Time course sequencing data analysis
Time course sequencing data analysis
Tools for making reports in various formats
Tools for making reports in various formats
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
Transcription Start Site Identification
Transcription Start Site Identification
Transcriptome-guided quality assessment of methylated RNA immunoprecipitation sequencing data
Two phase differential expression for singel-cell RNA-seq
uSORT: A self-refining ordering pipeline for gene selection
uSORT: A self-refining ordering pipeline for gene selection
uSORT: A self-refining ordering pipeline for gene selection
Varying-Censoring Aware Matrix Factorization
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
Visualization of multi-dimentional cancer genomics data
Visualization of multi-dimentional cancer genomics data
Visualization of multi-dimentional cancer genomics data
Zero-Inflated Negative Binomial Model for RNA-Seq Data
Zero-Inflated Negative Binomial Model for RNA-Seq Data