Biocview "RNASeq"

10X Genomics Chromium
10X Genomics Chromium
10X Genomics Chromium
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 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 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 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 using Multiple Corespondence Analysis
Analysis of Time-Resolved RNA-Seq Data
Analysis of Time-Resolved RNA-Seq 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 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 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 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
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
Assigning scRNA-seq to clone-of-origin using copy number from ultra-low-depth scDNA-seq
Assign Properties to TNBC Patients
Assign Properties to TNBC Patients
A 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 **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data
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 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
Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
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
bcbio Single-Cell RNA-Seq
bcbio Single-Cell 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
Bias Awared Peak Calling and Quantification for MeRIP-Seq
Bias Awared Peak Calling and Quantification for MeRIP-Seq
Big multivariate data plotted interactively
Big multivariate data plotted interactively
Big multivariate data plotted interactively
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
Calculate JCC Scores
Calculate strandness information of a bam file
Calculate strandness information of a bam file
Calculate strandness information of a bam file
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: A cluster-based approach for distinguishing cells from background barcodes in 10x Genomics data
Cell-Cycle using Mixture Models
Cell OrderiNg by FluorEScence Signal
Cell Signalling Using Single Cell RNAseq Data Analysis
Cell Signalling Using Single Cell RNAseq Data Analysis
Characterization of Alternative Splicing based on Paired-End Reads
Classify Samples From RNA-Seq Datasets
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 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 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
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
Controlling bias and inflation in association studies using the empirical null distribution
Coordinated Gene Activity in Pattern Sets
Coordinated Gene Activity in Pattern Sets
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
Decomposing Heterogeneous Cohorts using Omic Data Profiling
Decomposing Heterogeneous Cohorts using Omic Data Profiling
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 Analysis Utilities
DESeq2 Analysis Utilities
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 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
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 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 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
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 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)
Ensemble of Gene Set Enrichment Analyses
Ensemble of Gene Set Enrichment Analyses
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 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 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 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
Fast, Sensitive, and Accurate Integration of Single Cell Data
FCBF-based Co-Expression Networks for Single Cells
FCBF-based Co-Expression Networks for Single Cells
FCBF-based Co-Expression Networks for Single Cells
Filter replicated high-throughput transcriptome sequencing data
Filter replicated high-throughput transcriptome sequencing data
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: differential transcript and gene expression with inferential replicates
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 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 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
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
Gene regulator enrichment analysis
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
Genomic trajectories with heterogeneous genetic and environmental backgrounds
Global Test for Counts
Global Test for Counts
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Guitar
HDF5 backend for DelayedArray objects
HDF5 backend for DelayedArray objects
Hit counts and enrichment/depletion analysis tools for repeat elements
iASeq: integrating multiple sequencing datasets for detecting allele-specific events
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
Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.
Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.
Identify Differentially Expressed Genes from RNA-seq data
Identify genes associated with multiple expression phenotypes in single-cell CRISPR screening data
Identify genes associated with multiple expression phenotypes in single-cell CRISPR screening data
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 enables high-precision 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
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
Infers biological signatures from gene expression data
InPAS: a bioconductor package for the identification of novel alternative PolyAdenylation Sites (PAS) using RNA-seq 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
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 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
Intron-Exon Retention Estimator
Intron-Exon Retention Estimator
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: Beyond the traditional Transcriptomic pipeline
KnowSeq R/Bioc package: Beyond the traditional Transcriptomic pipeline
L1-regularization based methods for detection of differential splicing
L1-regularization based methods for detection of differential splicing
Landscape Single Cell Entropy
Laplacian eigenmaps & principal curves for pseudotemporal ordering of single-cell RNA-seq data
Linear model and normality based normalization and transformation method (Linnorm)
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
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
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
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-Omics Simulation (MOSim)
Multi-Omics Simulation (MOSim)
Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis
Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis
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
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
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
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
OUTRIDER - OUTlier in RNA-Seq fInDER
OUTRIDER - OUTlier in RNA-Seq fInDER
Overlay omics data onto SBGN pathway diagram
Overlay omics data onto SBGN pathway diagram
Overlay omics data onto SBGN pathway diagram
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
PCAtools: Everything Principal Components Analysis
PCAtools: Everything Principal Components Analysis
Permutation-Based Confidence for Molecular Classification
PhantomPurgeR
Pipeline for augmented co-expression analysis
pipeline for single cell RNA-seq data analysis
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
Prediction of pri-miRNA Transcription Start Site
Prediction of pri-miRNA Transcription Start Site
Prize: an R package for prioritization estimation based on analytic hierarchy process
Probe region expression estimation for RNA-seq data for improved microarray comparability
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
Quantification and Visulization of Variations of Splicing in Population
Quantification and Visulization of Variations of Splicing in Population
Quantification and Visulization 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 divers 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
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
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
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
RnaSeqSampleSize
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
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
scDataviz: single cell dataviz and downstream analyses
scDataviz: single cell dataviz and downstream analyses
scDblFinder
scDblFinder
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
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
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 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 toolkit
Single-cell RNA-seq toolkit
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-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 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
ssPATHS: Single Sample PATHway Score
ssPATHS: Single Sample PATHway Score
Statistical analysis of sequins
Statistical analysis of sequins
Subread Sequence Alignment and Counting for R
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
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: NGS workflow templates and sample data
systemPipeR: NGS workflow and report generation environment
systemPipeR: NGS workflow 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
this package collects r fxns useful in my daily coding life
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
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
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
Transcription Start Site Identification
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
Two phase differential expression for singel-cell RNA-seq
Two phase differential expression for single-cell RNA-seq
Unbiased Extraction of Single Cell Identity using Multiple Correspondence Analysis
Unbiased Extraction of Single Cell Identity using Multiple Correspondence Analysis
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
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
Weighted matrix manipulation, finding components of variation with weighted or sparse data
Weighted matrix manipulation, finding components of variation with weighted or sparse data
What the Package Does (One Line, Title Case)
What the Package Does (One Line, Title Case)
Wind: weighted indexes for clustering evaluation
XCI-inference
XCI-inference
Zero-Inflated Negative Binomial Model for RNA-Seq Data
Zero-Inflated Negative Binomial Model for RNA-Seq Data