Biocview "RNASeq"

A/B compartment inference from ATAC-seq and methylation array data

Acid Genomics DESeq2 Analysis Utilities

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

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

A List of Relevent Functions RNA-seq data analysis

alpine

A metric to determine the biological quality of gene clusters

A multi-tissue transcriptional age calculator

Analysis for short time-series data

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 Transposable Elements

Analysis Tools for 10X V(D)J Data

Analyze isomiRs and miRNAs from small RNA-seq

Analyze small RNA-seq count data

Analyze Transcription Factor Enrichment

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 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

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 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 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 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

ArrayExpress High Throughput Sequencing Processing Pipeline

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

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

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 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 Generic Cell Type Enrichment Analysis

A tool for unsupervised projection of single cell RNA-seq data

A toolkit for APA analysis using RNA-seq data

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 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

A visualization tool for single cell data of C.elegans embrogenesis

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

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 clustering and imputationa of single cell methylomes

Bayesian hierarchical mixture of factor analyzers for modelling genomic bifurcations

Bcbio RNA-Seq

Benchmarks for RNA-seq Quantification Pipelines

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

Biological Network Analysis

BioTIP: An R package for characterization of Biological Tipping-Point

Breakpoint analysis of time-course expression data

Brings Seurat to the Tidyverse

Brings SingleCellExperiment to the Tidyverse

Brings SummarizedExperiment to the Tidyverse

Brings transcriptomics to the tidyverse

Building Expression Atlas from RNA-Seq data

Calculate JCC Scores

Calculate strandness information of a bam file

Candidate Driver Analysis

Casc

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

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

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

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 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 of Time Series Gene Expression data

Co-Expression Analysis of Sequencing Data

Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis

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.

CommunityAMARETTO: A Computational Tool for the Discovery of Shared and Distinct Regulatory Mechanisms Across Biological Systems

Compare Characteristic Features of Count Data Sets

Compare Clusterings for Single-Cell Sequencing

Comparing Differential Abundance/Expression Methods

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

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

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

Coverage visualization package for R

Create, manipulate, visualize splicing graphs, and assign RNA-seq reads to them

Create rapid visualizations of RNAseq data in R

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 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

DegNorm: degradation normalization for RNA-seq data

Delineate outstanding genomic zones of differential gene activity

derfinder helper package

DESeq2 Wrapper For Pre-Specified Analyses

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

Detecting abberant splicing events from RNA-sequencing data

Detecting hidden batch factors through data adaptive adjustment for biological effects

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 Alternative Polyadenylation Analysis From Compositions

Differential cell-type-specific allelic imbalance

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 for RNA-seq data through a robust variance component test

Differential gene expression analysis based on the negative binomial distribution

Differential Gene Expression Analysis for Multi-subject scRNA-seq

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 Topology, Progression and Differentiation.

Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq

Discriminant Analysis for Evolutionary Inference

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

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 Method of Optimal Pvalue Weighting

Empirical RNA-seq Sample Size Analysis

Engineering Evaluation by Gene Categorization (eegc)

Enrichment Approach to Predict Which Transcription Factors are Regulated

Ensemble of Gene Set Enrichment Analyses

Estimate Promoter Activity from RNA-Seq data

Estimates Isoform Specific RPF Footprint Densities

eSVD2 for performing the eSVD-DE for cohort-wide differential expression analysis

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

exome-based anlaysis of MeRIP-Seq data: peak calling and differential analysis

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

Explore and download data from the recount3 project

Explore and download data from the recount project

Expression Weighted Celltype Enrichment

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 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

FCBF-based Co-Expression Networks for Single Cells

Filtering of Lowly Expressed Features

Filter replicated high-throughput transcriptome sequencing 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

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

Functions used to preprocess datasets stored in BioDataome

GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC

Gene Expression Meta-analysis Visualization Tool

Gene Expression Variation Analysis (GEVA)

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

General Sample Size and Power Analysis for Microarray and Next-Generation Sequencing Data

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 Summary Plots of FastQC Reports

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 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 / 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

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 User Interface for High Performance BAM-based binary alternative splicing event quantitation, differential analysis, and visualisation

Guitar

HDF5 backend for DelayedArray objects

HDF5 datasets as array-like objects in R

Heatmaps of Stack Profiles from Epigenetic Signals

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 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 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 likely duplicate samples from genomic or meta-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

Improving replicability in single-cell RNA-Seq cell type discovery

Independent Hypothesis Weighting

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

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

Integrating Cap Enrichment with Transcript Expression Analysis

Integrative analysis of Multi-omics data for Alternative Splicing

Integrative Statistics of alleLe Dependent Expression

interactive analysis and visualization of alternative splicing in R

Interactive Differential Expresion Analysis Browser

Interactive Differential Expression AnaLysis

Interactive HTML graphics

Interactive visualization in genomics

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

Interpretation of RNA-seq experiments through robust, efficient comparison to public databases

Introduction to Tidy Transcriptomics

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

JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data

kallisto | bustools R utilities

KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline

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

Low-Rank Factorization for Subspace-clustering

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 tools for automated transcriptome clustering analysis

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 correlating biclusters for gene expression data and associated methods

Maximum Likelihood Decay Modeling of RNA Degradation Data

Maximum rank reproducibility

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 to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape

Michaelis-Menten Modelling of Dropouts in single-cell RNASeq

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

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 Nested Effects Models

Model-based Analysis of Single Cell Transcriptomics

Model higher-order methylation profiles

Modeling RNA synthesis, processing and degradation with RNA-seq data

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)

Multiple Sample Peak Calling

Multiplexes Isobaric Mass Tagged-based Kinetics Data for Network Analysis

Multi-Scale Target Explorer

Multivariate and directional gene set testing

Mutation Mapping Analysis Pipeline for Pooled RNA-Seq

NanoString GeoMx Tools

NanoString nCounter Tools

Negative Binomial Additive Model for RNA-Seq Data

Negative Binomial Models to detect Differential Splicing

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

Obtain Raw Read Counts from RNASeq Data

Open Reading Frames in Genomics

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-aware and Count-based Compositional Analysis of Single-cell Data.

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

Parallel implmentation of bounded memory GEE

PatchseqMap

PathoStat Statistical Microbiome Analysis Package

Pathway Fingerprint Framework in R

PCAtools: Everything Principal Components Analysis

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 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

PolyA counting and differential transcript usage analysis for scRNA-seq data

Pooling RNA-seq datasets for assembling transcript models

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 combinding m6A reader binding information

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

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

Publication-ready volcano plots with enhanced colouring and labeling

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 Visulization of Variations of Splicing in Population

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

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

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

Remove Unwanted Variation from RNA-Seq Data

Report of DEG analysis

Representation and manipulation of short genomic alignments

Reproducibility-Optimized Test Statistic

Reproducible GSEA Benchmarking

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

RNASeqR: an R package for automated two-group RNA-Seq analysis workflow

RnaSeqSampleSize

rnaSeq secondary analyses

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

Sample Classifier

Sample Size Calculation for RNA-Seq Experimental Design

Sample size for RNAseq studies

"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"

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

scDblFinder

sciCNV

scMerge: Merging multiple batches of scRNA-seq data

scRecover for imputation of single-cell RNA-seq data

Seamless navigation through combined results of set-based and network-based enrichment analysis

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

Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size

SigFuge

Significance-based Modules Integrating the Transcriptome and Epigenome

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 Batch Correction Methods

Single-Cell Consensus Clustering

Single Cell Differential Expression

Single Cell Entropy

single-cell higher order testing

Single Cell Overview of Normalized Expression data

Single-Cell RNA-Seq Analysis Utilities

Single-cell RNA sequencing data normalization

Single Cell RNA-Seq UMI Filtering Facilitator (scruff)

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

SMNN: Batch Effect Correction for Single-cell RNA-seq data with Supervised Mutual Nearest Neighbor Detection

Smooth quantile normalization

Sparse Contrastive Principal Component Analysis

Spatial Overlay for Omic Data from Nanostring GeoMx Data

Spatial Transcriptomics Analysis

Splice event prediction and quantification from RNA-seq data

Splice Interpreter of Transcripts

Splicing Diversity Analysis for Transcriptome Data

SpotClean adjusts for spot swapping in spatial transcriptomics data

ssPATHS: Single Sample PATHway Score

Stan implementation of BASiCS

Statistical analysis of RNA editing sites and hyper-editing regions

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

Suffix Array Kernel Smoothing for discovery of correlative sequence motifs and multi-motif domains

Suite of Functions for Pooled Crispr Screen QC and Analysis

Summarization and expression/phenotype association of CNV ranges

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

systemPipeRdata: Workflow templates and sample data

systemPipeR: NGS workflow and report generation environment

systemPipeR: Workflow Environment for Data Analysis and Report Generation

Targeted Learning with Moderated Statistics for Biomarker Discovery

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 Discordant Method: A Novel Approach for Differential Correlation

The Genomic STate ANnotation Package

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

Tomo-seq data analysis

Toolbox for mRNA epigenetics sequencing analysis

Tools for Assessing Clustering

Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data

Tools for making reports in various formats

Tools for Managing Seurat Objects

Tools for matrices with precision weights, test and explore weighted or sparse data

Tools for Omics Data Analysis

Tools for ordering single-cell sequencing

Tools for spliced gene structure manipulation and analysis

Tools for the Efficient Analysis of High-Resolution Genomics Data

Top Confident Effect Sizes

Topology-based pathway analysis of RNA-seq 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 Rewiring

Transcription Start Site Identification

Transcriptome CUTteR

Transcriptome-guided quality assessment of m6A-seq data

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

Unified statistal Modeling of Omics Data

uORF prediction in R

User Friendly Single-Cell and Bulk RNA Sequencing Visualization

uSORT: A self-refining ordering pipeline for gene selection

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 EHT Data

Visual and interactive gene expression analysis

Visual Exploration of Omic Datasets Using a Shiny App

Visualise microarray and RNAseq data using gene ontology annotations

Visualization of multi-dimentional cancer genomics data

What the Package Does (One Line, Title Case)

Wind: weighted indexes for clustering evaluation

Workflow for constructing Pathway-Gene-Transcript expression networks

XCI-inference

Zero-Inflated Negative Binomial Model for RNA-Seq Data

Biocview "RNASeq"

R Package Documentation

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