Biocview "RNASeq"

A/B compartment inference from ATAC-seq and methylation array data
Acid Genomics DESeq2 Analysis Utilities
Acid Genomics DESeq2 Analysis Utilities
Acid Genomics DESeq2 Analysis Utilities
A collection of single-cell V(D)J tools
A collection of single-cell V(D)J tools
A correlation-based method for quality filtering of single-cell RNAseq data
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 fast hierarchical graph-based clustering method
A Fast Scalable and Flexible Non Negative Matrix Factorization Method
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
AIPS : Absolute Inference of Patient Signatures
Alikeness Based on Regression on Transciptome DECOnvolution
Alikeness Based on Regression on Transciptome DECOnvolution
A List of Relevent Functions RNA-seq data analysis
alpine
alpine
A metric to determine the biological quality of gene clusters
A multi-tissue transcriptional age calculator
A multi-tissue transcriptional age calculator
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 Alternative Splicing Using RNA-Seq
Analysis of amplicon enrichment panels
Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account
Analysis Of Differential Abundance Taking Sample Variation Into Account
Analysis of Time-Resolved RNA-Seq Data
Analysis of Time-Resolved RNA-Seq Data
Analysis of Transposable Elements
Analysis Tools for 10X V(D)J Data
Analyze isomiRs and miRNAs from small RNA-seq
Analyze isomiRs and miRNAs from small RNA-seq
Analyze small RNA-seq count data
Analyze Transcription Factor Enrichment
Analyze Transcription Factor Enrichment
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 Interactive Consensus Clustering Framework for Multi-platform Data Analysis
An Interactive Consensus Clustering Framework for Multi-platform Data Analysis
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
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 package for identification of novel peptides by customized database derived from RNA-Seq
An R interface for computational modeling of tumor progression
An R interface for computational modeling of tumor progression
An R package facilitating analysis of RNA modifications, structures, and interactions
An R package facilitating analysis of RNA modifications, structures, and interactions
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 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 easy provision of simple but complete tab-delimited genomic annotation from a variety of sources and organisms
An R Package for Time Course RNASeq Data Analysis
An R Package for Unbiased Splicing Pathway Analysis
An R Package for Unbiased Splicing Pathway Analysis in RNAseq data
A package for variant peptides detection and visualization in shotgun proteomics.
A Package to Download, Organize and Analyze Genomic Data Commons (GDC) Data
Approximate posterior estimation for GLM coefficients
Approximate posterior estimation for GLM coefficients
ArrayExpress High Throughput Sequencing Processing Pipeline
ArrayExpress High Throughput Sequencing Processing Pipeline
A search tool for single cell RNA-seq data by gene lists
A search tool for single cell RNA-seq data by gene lists
A Shiny App to accompany clusterExperiment
askoR - Differential Expresion Analysis using edgeR
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
Assessment of duplication rates in RNA-Seq datasets
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
Association Plots
Association Plots
Association Plots
A Statistical Framework for Modeling and Identifying Differential Distributions in Single-cell RNA-sequencing Data
A suite of functions to facilitate zFPKM transformations
A suite of functions to facilitate zFPKM transformations
A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data
A Supervised Approach for Predicting Cell Cycle Progression Using Single-Cell RNA-seq Data
Asymmetric Within-Sample Transformation
A Tidy Transcriptomics introduction to RNA-Seq analyses
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 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 unified computational framework for genomic feature annotation, differential expression analysis of circular RNAs
Automated, probabilistic assignment of scRNA-seq to cell types
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
BANDITS: Bayesian ANalysis of DIfferenTial Splicing
BANDITS: Bayesian ANalysis of DIfferenTial Splicing
Barycenter Single-Cell Differential Expression for Case-Control Studies
Base NanoString Experiment Class
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 of Differential Expression in RNA Sequencing Data
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
Bcbio RNA-Seq
Bcbio RNA-Seq
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
Bias Awared Peak Calling and Quantification for MeRIP-Seq
Big multivariate data plotted interactively
Bioinformatics pipelines based on Rcwl
Bioinformatics pipelines based on Rcwl
Bioinformatics pipelines based on Rcwl
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
Breakpoint analysis of time-course expression data
Breakpoint analysis of time-course expression data
Brings Seurat to the Tidyverse
Brings Seurat to the Tidyverse
Brings SingleCellExperiment to the Tidyverse
Brings SingleCellExperiment to the Tidyverse
Brings SingleCellExperiment to the Tidyverse
Brings SummarizedExperiment to the Tidyverse
Brings SummarizedExperiment to the Tidyverse
Brings SummarizedExperiment to the Tidyverse
Brings transcriptomics to the tidyverse
Brings transcriptomics to the tidyverse
Brings transcriptomics to the tidyverse
Brings transcriptomics to the tidyverse
Building Expression Atlas from RNA-Seq data
Building Expression Atlas from RNA-Seq data
Building Expression Atlas from RNA-Seq data
Building Expression Atlas from RNA-Seq data
Calculate JCC Scores
Calculate strandness information of a bam file
Calculate strandness information of a bam file
Calculate strandness information of a bam file
Candidate Driver Analysis
Candidate Driver Analysis
Casc
Category encoding method for selecting feature genes for the classification of single-cell RNA-seq
Category encoding method for selecting feature genes for the classification of single-cell RNA-seq
Causal network analysis methods
CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data
CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data
ccImpute: an accurate and scalable consensus clustering based approach to impute dropout events in the single-cell RNA-seq data
ccImpute: an accurate and scalable consensus clustering based approach to impute dropout events in the single-cell RNA-seq data (https://doi.org/10.1186/s12859-022-04814-8)
Cell-Cycle using Mixture Models
Cell OrderiNg by FluorEScence Signal
CellRanger Input/Output
Cell Signalling Using Single Cell RNAseq Data Analysis
Cell Signalling Using Single Cell RNAseq Data Analysis
Characterization of Alternative Splicing based on Paired-End Reads
CircRNA transcriptome assembly tool
Classify Samples From RNA-Seq Datasets
Clone Identification from Single Cell Data
Clone Identification from Single Cell Data
Clone Identification from Single Cell Data
Cluster analysis of Spatial Transcriptomics data
Cluster analysis of Spatial Transcriptomics data
Clustering and pathway analysis using exponential distributions
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 Deviation Index (CDI)
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
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
Colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity
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.
CommunityAMARETTO: A Computational Tool for the Discovery of Shared and Distinct Regulatory Mechanisms Across Biological Systems
Compare Characteristic Features of Count Data Sets
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
Comparing Differential Abundance/Expression Methods
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
Context-Aware Transcript Quantification from Long Read RNA-Seq data
Controlling bias and inflation in association studies using the empirical null distribution
Coordinated Gene Activity in Pattern Sets
Coordinated Gene Activity in Pattern Sets
Core Engine for NxtIRF: a User-Friendly Intron Retention and Alternative Splicing Analysis using the IRFinder Engine
Count summarization and normalization for RNA-Seq data
Covariate Assisted Large-scale Multiple testing
Covariate Assisted Large-scale Multiple testing
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
Create rapid visualizations of RNAseq data in R
Create rapid visualizations of RNAseq data in R
Create rapid visualizations of RNAseq data in R
Create rapid visualizations of RNAseq data in R
Cross-platform consensus analysis of genomic measurements via interlaboratory testing method
Cross-platform consensus analysis of genomic measurements via interlaboratory testing method
Cut rDNA Sequences Into Domains Using Covariance Models
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 resource for package "TRESS"
Data structures, clustering and testing for single cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)
Decomposing Heterogeneous Cohorts using Omic Data Profiling
Decomposing Heterogeneous Cohorts using Omic Data Profiling
DegNorm: degradation normalization for RNA-seq data
DegNorm: degradation normalization for RNA-seq data
Delineate outstanding genomic zones of differential gene activity
Delineate outstanding genomic zones of differential gene activity
derfinder helper package
derfinder helper package
DESeq2 Wrapper For Pre-Specified Analyses
DESeq2 Wrapper For Pre-Specified Analyses
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
Detecting abberant splicing events from RNA-sequencing data
Detecting abberant splicing events from RNA-sequencing data
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
Determination of essential phenotypic elements of clusters in high-dimensional entities
Determination of essential phenotypic elements of clusters in high-dimensional entities
DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates
dgeAnalysis
dgeAnalysis
Differential Alternative Polyadenylation Analysis From Compositions
Differential cell-type-specific allelic imbalance
Differential Co-expression Analysis
Differential Co-expression Analysis
Differential Expression Analysis based on the read count data generated by either of Salmon, Kallisto, featureCounts and perform statistical analysis to discover quantitative changes in expression levels between two different experimental groups
Differential Expression Analysis based on the read count data generated by either of Salmon, Kallisto, featureCounts and perform statistical analysis to discover quantitative changes in expression levels between two different experimental groups
Differential Expression Analysis for RNA-seq data through a robust variance component test
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 Analysis for Multi-subject scRNA-seq
Differential Gene Expression Analysis for Multi-subject scRNA-seq
Differential gene expression data formats converter
Differential gene expression data formats converter
Differentially Expressed Gene-Gene pairs
Differentially regulated genes from scRNA-seq data
Differential pattern analysis for Ribo-seq data
Differential pattern analysis for Ribo-seq data
Differential Topology, Progression and Differentiation
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
Discriminant Analysis for Evolutionary Inference
Discriminant Analysis for Evolutionary Inference
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
Downloads ENA Fastqs With GEO Accessions
Easy Analysis of RNASeq DE
Easy Analysis of RNASeq DE
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 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 Method of Optimal Pvalue Weighting
Empirical RNA-seq Sample Size Analysis
Empirical RNA-seq Sample Size Analysis
Engineering Evaluation by Gene Categorization (eegc)
Engineering Evaluation by Gene Categorization (eegc)
Enrichment Approach to Predict Which Transcription Factors are Regulated
Ensemble of Gene Set Enrichment Analyses
Ensemble of Gene Set Enrichment Analyses
Estimate Promoter Activity from RNA-Seq data
Estimate Promoter Activity from RNA-Seq data
Estimates Isoform Specific RPF Footprint Densities
EWCE for Multiple Gene Lists
Example experimental microarray data set for the "biotmle" R package
ExCluster robustly detects differentially expressed exons between two conditions of RNA-seq data, requiring at least two independent biological replicates per condition
ExCluster robustly detects differentially expressed exons between two conditions of RNA-seq data, requiring at least two independent biological replicates per condition
exome-based anlaysis of MeRIP-Seq data: peak calling and differential analysis
Exon-Intron Split Analysis (EISA) in R
Exon-Intron Split Analysis (EISA) in R
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
Explore and download data from the recount3 project
Explore and download data from the recount3 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
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
Fast and accurate scRNA-seq cell type identification
Fast and accurate scRNA-seq cell type identification
Fast and Interpretable Consensus Clustering via Minipatch Learning
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
FCBF-based Co-Expression Networks for Single Cells
FCBF-based Co-Expression Networks for Single Cells
FCBF-based Co-Expression Networks for Single Cells
Filtering of Lowly Expressed Features
Filter replicated high-throughput transcriptome sequencing data
Filter replicated high-throughput transcriptome sequencing data
Find RAre Splicing Events in RNA-Seq Data
Find RAre Splicing Events in RNA-Seq Data
Find RAre Splicing Events in RNA-Seq Data
Fishpond: differential transcript and gene expression with inferential replicates
Fishpond: downstream methods and tools for expression data
Fit a Gamma-Poisson Generalized Linear Model
Fit a Gamma-Poisson Generalized Linear Model
Flexible, isoform-level differential expression analysis
Flexible, isoform-level differential expression analysis
Flexible, isoform-level differential expression analysis
functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets
Functional interpretation of single cell RNA-seq latent manifolds
Functional interpretation of single cell RNA-seq latent manifolds
Functions used to preprocess datasets stored in BioDataome
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
Gene Expression Meta-analysis Visualization Tool
Gene Expression Meta-analysis Visualization Tool
Gene Expression Variation Analysis (GEVA)
Gene Expression Variation Analysis (GEVA)
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
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
General Sample Size and Power Analysis for Microarray and Next-Generation Sequencing Data
Generate 'BART' File
Generate 'BART' File
Generate 'BART' File
Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search
Generate customized protein databases from NGS 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 Summary Plots of FastQC Reports
Generating Tree Hierarchy Visualizations from Gene Expression Data
Generating Tree Hierarchy Visualizations from Gene Expression Data
Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences
Generation of null ranges via bootstrapping or covariate matching
Gene regulator enrichment analysis
Gene regulator enrichment analysis
Gene set analysis accounting for gene-gene correlations
Gene set analysis following differential expression using linear (mixed) modeling with dream
Gene Set Enrichment Analysis Extended to Contingency Cubes
Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
Gene Set Enrichment / Projection Displays
Gene Set Enrichment / Projection Displays
Gene Set Variation Analysis for Microarray and RNA-Seq Data
Genomic trajectories with heterogeneous genetic and environmental backgrounds
GEOexplorer: a webserver for gene expression analysis and visualisation
GEOexplorer: a webserver for gene expression analysis and visualisation
GEOexplorer: a webserver for gene expression analysis and visualisation
Global Test for Counts
Global Test for Counts
GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Graphical User Interface for High Performance BAM-based binary alternative splicing event quantitation, differential analysis, and visualisation
Guitar
Guitar
HDF5 backend for DelayedArray objects
HDF5 backend for DelayedArray objects
Heatmaps of Stack Profiles from Epigenetic Signals
Helper Functions for LIBD Deconvolution
Helper Functions for LIBD Deconvolution
Higher-order chromatin domain inference in single samples from methylation arrays and single cells from scRNA-seq and scATAC-seq
Higher-order chromatin domain inference in single samples from methylation arrays and single cells from scRNA-seq and scATAC-seq
Higher-Order Deconvolution Survival Analyses
Hit counts and enrichment/depletion analysis tools for repeat elements
iASeq: integrating multiple sequencing datasets for detecting allele-specific events
Identification and analysis of miRNA sponge regulation
Identification and analysis of miRNA sponge regulation
Identification of candidate causal perturbations from differential gene expression data
Identification of candidate causal perturbations from differential gene expression data
Identification of genetic Variants affecting Alternative Splicing
Identifies differentially expressed genes with respect to other local genes
Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.
Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data
Identify Differentially Expressed Genes from RNA-seq data
Identify genes associated with multiple expression phenotypes in single-cell CRISPR screening data
Identify genes associated with multiple expression phenotypes in single-cell CRISPR screening 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
ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data
ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data
ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data
ImagingAMARETTO: tools for interpreting multi-omics networks for relevance to clinical outcomes and radiographic and histopathology imaging-derived biomarkers
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
Independent Hypothesis Weighting
Independent Hypothesis Weighting
Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis
Individualized Multi-Omic Pathway Deviation Scores Using Multiple Factor Analysis
Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure
Inference of differential exon usage in RNA-Seq
Inference of differential exon usage in RNA-Seq
Inferring the Tree of Cells
Inferring unobserved perturbations from gene expression data
Infers biological signatures from gene expression data
InPAS: a bioconductor package for the identification of novel alternative PolyAdenylation Sites (PAS) using RNA-seq data
In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data
In-Silico Annotation of Doublets for Single Cell RNA Sequencing 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 Statistics of alleLe Dependent Expression
Integrative Statistics of alleLe Dependent Expression
interactive analysis and visualization of alternative splicing in R
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 visualization in genomics
Interactive visualization in genomics
Interactive Visualization of RNA-seq Data Using a Principal Components Approach
Interactive Visualization of RNA-seq Data Using a Principal Components Approach
Interface to Call Programs from Infernal RNA Covariance Model Package
Interpretable marker-based single-cell pseudotime using Bayesian parametric models
Interpretable marker-based single-cell pseudotime using Bayesian parametric models
Interpretation of RNA-seq experiments through robust, efficient comparison to public databases
Interpretation of RNA-seq experiments through robust, efficient comparison to public databases
Introduction to Tidy Transcriptomics
Introduction to Tidy Transcriptomics
Introduction to Tidy Transcriptomics
Introduction to Tidy Transcriptomics
Introduction to Tidy Transcriptomics
Introduction to Tidy Transcriptomics
Introduction to Tidy Transcriptomics
Introduction to Tidy Transcriptomics
Intron-Exon Retention Estimator
Intron-Exon Retention Estimator
IReNA
iSMNN: Batch Effect Correction for Single-cell RNA-seq data via Iterative Supervised Mutual Nearest Neighbor Refinement
Isoform expression estimation based on RNA-seq data
Iteratively Adjusted Surrogate Variable Analysis
Iteratively Adjusted Surrogate Variable Analysis
Iteratively Adjusted Surrogate Variable Analysis
JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data
kallisto | bustools R utilities
kallisto | bustools R utilities
kallisto | bustools R utilities
KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline
KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline
L1-regularization based methods for detection of differential splicing
L1-regularization based methods for detection of differential splicing
Label-Free Identification of Endogenous Informative Single Cell Mitochondrial RNA Mutation for Lineage Analysis and Clonal Evolution
Landscape Single Cell Entropy
Laplacian eigenmaps & principal curves for pseudotemporal ordering of single-cell RNA-seq data
Large-scale single-cell RNA-seq data manipulation with GDS files
Linear model and normality based normalization and transformation method (Linnorm)
Linear Models for Microarray Data
Linear Models for Microarray Data
Low-Rank Factorization for Subspace-clustering
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
m6Aexpress-BHM: Predicting m6A regulation of gene expression in multiple-groups context by a Bayesian Hierarchical Mixture model
Machine Learning Interface for RNA-Seq Data
Machine Learning Interface for RNA-Seq Data
Machine Learning Interface for RNA-Seq Data
Machine learning tools for automated transcriptome clustering analysis
Make read coverage plots from BigWig files
Make read coverage plots from BigWig files
Mapping, quantification and variant analysis of sequencing data
Marker Gene Finder in RNA-seq data
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
Maximum rank reproducibility
Maximum rank reproducibility
megadepth: BigWig and BAM related utilities
megadepth: BigWig and BAM related utilities
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 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
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
Minimized Single-Cell Consensus Clustering
Minimized Single-Cell Consensus Clustering
MiRNA Ranking by Gene Expression
Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions
Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions
Mixture Nested Effects Models
Mixture Nested Effects Models
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 RNA synthesis, processing and degradation with RNA-seq data
Modeling RNA synthesis, processing and degradation with RNA-seq data
Monte Carlo Reference-based Consensus Clustering
Monte Carlo Reference-based Consensus Clustering
Multi-Modal Single-Cell Analysis Methods
Multi-omics Classification, Functional Enrichment and Network Inference analysis
Multi-Omics Simulation (MOSim)
Multi-Omics Simulation (MOSim)
Multiple Sample Peak Calling
Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis
Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis
Multi-Scale Target Explorer
Multivariate and directional gene set testing
Multivariate and directional gene set testing
Mutation Mapping Analysis Pipeline for Pooled RNA-Seq
Mutation Mapping Analysis Pipeline for Pooled RNA-Seq
Mutation Mapping Analysis Pipeline for Pooled RNA-Seq
NanoString GeoMx Tools
NanoString nCounter Tools
Negative Binomial Additive Model for RNA-Seq Data
Negative Binomial Additive Model for RNA-Seq Data
Negative Binomial Models to detect Differential Splicing
Negative Binomial Models to detect Differential Splicing
Network smoothing for scRNAseq
Network smoothing for scRNAseq
NEUral network-based single-Cell Annotation tool
Normalization of Single-Cell mRNA Sequencing Data
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
Open Reading Frames in Genomics
Open Reading Frames in Genomics
Open Reading Frames in Genomics
Optimal p-value weighting with independent information
Optimal p-value weighting with independent information
Optimising the Definition of Expressed Regions
Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq
Outlier Analysis for pairwise differential comparison
Outlier Analysis for pairwise differential comparison
Outlier Analysis for pairwise differential comparison
Outlier-aware and Count-based Compositional Analysis of Single-cell Data.
OUTRIDER - OUTlier in RNA-Seq fInDER
OUTRIDER - OUTlier in RNA-Seq fInDER
Overlay omics data onto SBGN pathway diagram
Packaging common Seurat analysis tasks
PAIRADISE: Paired analysis of differential isoform expression
PAIRADISE: Paired analysis of differential isoform expression
Parallel implmentation of bounded memory GEE
PatchseqMap
PathoStat Statistical Microbiome Analysis Package
PathoStat Statistical Microbiome Analysis Package
Pathway Fingerprint Framework in R
PCAtools: Everything Principal Components Analysis
PCAtools: Everything Principal Components Analysis
Peak Calling and differential analysis for MeRIP-Seq
Peak Calling and differential analysis for MeRIP-Seq
Perform co-DE gene analysis
Permutation-Based Confidence for Molecular Classification
PhantomPurgeR
Pipeline for augmented co-expression analysis
Pipeline for augmented co-expression analysis
Pipeline for single cell multi-omic data pre-processing
pipeline for single cell RNA-seq data analysis
Pipeline tools for RNA-seq or ChIP-seq data
Plots of Statistics Collected by Qualimap from RNASeq Data
Plotting functions for derfinder
Plotting functions for derfinder
PolyA counting and differential transcript usage analysis for scRNA-seq data
Pooling RNA-seq datasets for assembling transcript models
Pooling RNA-seq datasets for assembling transcript models
Power Estimation Tool for RNA-Seq and proteomics data
Power Estimation Tool for RNA-Seq and proteomics data
Predicting context-specific m6A regulation of gene expression
Predicting context-specific m6A regulation of gene expression
Predicting context-specific m6A regulation of gene expression combinding m6A reader binding information
Prediction of pri-miRNA Transcription Start Site
Prediction of pri-miRNA Transcription Start Site
Predict MicroExons in Plant Genomes
Predict open reading frames in nucleotide sequences
Preprocessing, analyzing, and reporting of RNA-seq data
Prize: an R package for prioritization estimation based on analytic hierarchy process
Probabilistic Outlier Identification for RNA Sequencing Generalized Linear Models
Probabilistic Outlier Identification for RNA Sequencing Generalized Linear Models
Probe region expression estimation for RNA-seq data for improved microarray comparability
Processing Various Types of Data on GEO and TCGA
PROspective Power Evaluation for RNAseq
PROspective Power Evaluation for RNAseq
Publication-ready volcano plots with enhanced colouring and labeling
Publication-ready volcano plots with enhanced colouring and labeling
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 of Normalized Gene Expression Data
Quantification and Visualization of Variations of Splicing in Population
Quantification and Visualization of Variations of Splicing in Population
Quantification and Visualization of Variations of Splicing in Population
Quantification and Visualization of Variations of Splicing in Population
Quantification and Visulization of Variations of Splicing in Population
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 drivers of variation in multilevel gene expression experiments
qusage: Quantitative Set Analysis for Gene Expression
qusage: Quantitative Set Analysis for Gene Expression
Random Rotation Methods for High Dimensional Data with Batch Structure
Random Rotation Methods for High Dimensional Data with Batch Structure
Rank Constrained Similarity Learning for single cell RNA sequencing data
Rank Constrained Similarity Learning for Single Cell RNA Sequencing 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
Rcpp Integration Surrogate Variable Analysis
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
Reference-free Cell-Type Deconvolution of Multi-Cellular Spatially Resolved Transcriptomics Data
Reference-guided isoform reconstruction and quantification for long read RNA-Seq data
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression
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
Remove Unwanted Variation from RNA-Seq Data
Remove Unwanted Variation from RNA-Seq Data
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
Reproducible GSEA Benchmarking
Reproducible GSEA Benchmarking
Retrieves Condition-Specific Variants in RNA-Seq Data
Retrieves Condition-Specific Variants in RNA-Seq Data
RiboseQC, a Comprehensive Ribo-Seq Analysis Tool
'rifi' analyses data from rifampicin time series created by microarray or RNAseq
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
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
RNASeqR: an R package for automated two-group RNA-Seq analysis workflow
RnaSeqSampleSize
RnaSeqSampleSize
rnaSeq secondary analyses
RNA-Seq Utilities
RNA-Seq Utilities
Robust Outlier-aware Estimation of Composition and Heterogeneity for Single-cell Data
R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data
SAFE-clustering:Single-cell Aggregated (From Ensemble) Clustering for Single-cell RNA-seq Data
SAME: Single-cell RNA-seq Aggregated clustering via Mixture model Ensemble for 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
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
"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"
"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"
Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications
Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications
Scalable differential expression analysis of single cell transcriptomics datasets with complex study designs
Scaling normalization based on the Pareto distribution
scDataviz: single cell dataviz and downstream analyses
scDataviz: single cell dataviz and downstream analyses
scDataviz: single cell dataviz and downstream analyses
scDblFinder
scDblFinder
sciCNV
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
Segvis: A package for visualization of high throughput sequencing data along genomic segments
Semi-parametric simulation tool for bulk and single-cell RNA sequencing data
Semi-parametric simulation tool for bulk and single-cell RNA sequencing data
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
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
Simple Simulation of Single-cell RNA Sequencing Data
Simple Simulation of Single-cell RNA Sequencing Data
Simulate Bulk RNA-seq Datasets from Single-Cell Datasets
Simulation and Deconvolution of Omic Profiles
Single-cell analysis toolkit for gene expression data in R
Single-Cell Analysis Toolkit for Gene Expression Data in R
Single-Cell 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 Consensus Clustering
Single-Cell Consensus Clustering
Single Cell Differential Expression
Single Cell Differential Expression
Single Cell Entropy
single-cell higher order testing
single-cell higher order testing
Single Cell Overview of Normalized Expression data
Single Cell Overview of Normalized Expression data
Single-Cell RNA-Seq Analysis Utilities
Single-Cell RNA-Seq Analysis Utilities
Single-cell RNA sequencing data normalization
Single-cell RNA sequencing data normalization
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single-Cell RNA-Seq Utilities
Single-Cell RNA-Seq Utilities
Single-cell Targetted Network Inference
Single-Cell UTR Bootstrap Tools
Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
Small-Count Analysis Methods for High-Dimensional Data
Small-Count Analysis Methods for High-Dimensional Data
SMNN: Batch Effect Correction for Single-cell RNA-seq data with Supervised Mutual Nearest Neighbor Detection
Smooth quantile normalization
Smooth quantile normalization
Sparse Contrastive Principal Component Analysis
Sparse Contrastive Principal Component Analysis
Spatial Overlay for Omic Data from Nanostring GeoMx Data
Spatial Transcriptomics Analysis
Spatial Transcriptomics Analysis
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
Splicing Diversity Analysis for Transcriptome Data
Splicing Diversity Analysis for Transcriptome Data
SpotClean adjusts for spot swapping in spatial transcriptomics data
ssPATHS: Single Sample PATHway Score
ssPATHS: Single Sample PATHway Score
ssPATHS: Single Sample PATHway Score
Stan implementation of BASiCS
Statistical analysis of RNA editing sites and hyper-editing regions
Statistical analysis of RNA editing sites and hyper-editing regions
Statistical analysis of sequins
Statistical analysis of sequins
Statistical methods for analysing single cell RNA-seq data
Statistical Utility for RBP (RNA binding protein) Functions
Structure Learning for Count Data
Subsampling of high-throughput sequencing count data
Subsampling of high-throughput sequencing count data
Suffix Array Kernel Smoothing for discovery of correlative sequence motifs and multi-motif domains
Suite of Functions for Pooled Crispr Screen QC and Analysis
Suite of Functions for Pooled Crispr Screen QC and Analysis
Suite of Functions for Pooled Crispr Screen QC and Analysis
Summarization and expression/phenotype association of CNV ranges
Summarization and expression/phenotype association of CNV ranges
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 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
systemPipeRdata: Workflow templates and sample data
systemPipeR: NGS workflow and report generation environment
systemPipeR: workflow management and report generation environment
Targeted Learning with Moderated Statistics for Biomarker Discovery
Targeted Learning with Moderated Statistics for Biomarker Discovery
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
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 Genomic STate ANnotation Package
The tidyomics blog
The tidyomics blog
this package collects r fxns useful in my daily coding life
Tidy Transcriptomics for Single-cell RNA Sequencing Analyses
Time course sequencing data analysis
Time course sequencing data analysis
Tomo-seq data analysis
Tomo-seq data analysis
Toolbox for mRNA epigenetics sequencing analysis
Toolbox for mRNA epigenetics sequencing analysis
Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data
Tools for making reports in various formats
Tools for making reports in various formats
Tools for matrices with precision weights, test and explore weighted or sparse data
Tools for matrices with precision weights, test and explore weighted or sparse data
Tools for Omics Data Analysis
Tools for Omics Data Analysis
Tools for ordering single-cell sequencing
Tools for ordering single-cell sequencing
Tools for spliced gene structure manipulation and analysis
Tools for spliced gene structure manipulation and analysis
Tools for the Efficient Analysis of High-Resolution Genomics Data
Tools for the Efficient Analysis of High-Resolution Genomics Data
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
Trajectory functions for visualization and interpretation.
Transcript abundance linear modeling from compressed coverage information
Transcript expression inference and differential expression analysis for RNA-seq data
Transcriptional analysis based on transcriptograms
Transcriptional analysis based on transcriptograms
Transcriptional Rewiring
Transcription Start Site Identification
Transcriptome CUTteR
Transcriptome-guided quality assessment of m6A-seq data
Transcript Quantification Import with Automatic Metadata
Transcript Quantification Import with Automatic Metadata
Translational control assessment from ribosome footprint and total RNA libraries
tricycle: Transferable Representation and Inference of cell cycle
Tumor heterogeneity level evaluation
Two phase differential expression for singel-cell RNA-seq
Two phase differential expression for single-cell RNA-seq
Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis
Unbiased Extraction of Single Cell Identity using Multiple Correspondence Analysis
Unbiased Extraction of Single Cell Identity using Multiple Correspondence Analysis
Unbiased Extraction of Single Cell Identity using Multiple Correspondence Analysis
Unified Statistal Modeling of Omics Data
Unified Statistal Modeling of Omics Data
uORF prediction in R
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
uSORT: A self-refining ordering pipeline for gene selection
uSORT: A self-refining ordering pipeline for gene selection
Utilities for Handling Single-Cell Droplet Data
Utilities for Handling Single-Cell Droplet Data
Varying-Censoring Aware Matrix Factorization
VeloViz: RNA-velocity informed 2D embeddings for visualizing cell state trajectories
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 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
What the Package Does (One Line, Title Case)
What the Package Does (One Line, Title Case)
Wind: weighted indexes for clustering evaluation
Workflow for constructing Pathway-Gene-Transcript expression networks
Workflow for constructing Pathway-Gene-Transcript expression networks
XCI-inference
XCI-inference
Zero-Inflated Negative Binomial Model for RNA-Seq Data
Zero-Inflated Negative Binomial Model for RNA-Seq Data