Bioconductor Topics

Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data

Inference of gene regulatory networks from gene expression data

KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline

Michaelis-Menten Modelling of Dropouts in single-cell RNASeq

Model-based Analysis of Single Cell Transcriptomics

MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks

Multi Omic Master Regulator Analysis

Shiny-based interactive data-quality exploration for omics data

Single cell replicability analysis

Prioritising a molecule-level storage of Spatial Transcriptomics Data

NanoString nCounter Tools

Negative binomial model for scRNA-seq

OSTA book data

OUTRIDER - OUTlier in RNA-Seq fInDER

OmniPath web service client and more

piRNA Cluster Builder

Poisson Identification of PEaks from Term-Seq data

Infers biological signatures from gene expression data

RNA Centric Annotation System

RFGeneRank: Cross-validated Stable Predictive Gene Ranking for Transcriptomics

Interactive web application for Omics-data analysis

R package for RIVER (RNA-Informed Variant Effect on Regulation)

Maximum Likelihood Decay Modeling of RNA Degradation Data

RNA Coverage-Shape-Based Quality Control Metrics

Rank-based reference mapping for fast and robust cell type annotation in spatial and single-cell transcriptomics

RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions

Client for the Reactome Analysis Service for comparative multi-omics gene set analysis

Gene regulator enrichment analysis

Investigating regions of interest and performing regional cell type-specific analysis with spatial transcriptomics data

Single-Cell Consensus Clustering

Single Cell Ecological Taxonomic Analysis

Rasterization Preprocessing Framework for Scalable Spatial Omics Data Analysis

Calculates cell type specificity from single cell data

Sparse Partial Correlations On Gene Expression

Statistical Transcriptome Analysis under a Dynamic Unified Model

Identification of Tumor-Discriminating mRNA Signatures via Support Vector Machines Supported by Disease Ontology

Predicting cell states and their variability in single-cell or spatial omics data

Filtering of Lowly Expressed Features

Calculate Pathway Scores for Each Cell in scRNA-Seq Data

S4 Class for Single Cell Data with Allele and Functional Levels for Immune Genes

Cell Signalling Using Single-Cell RNA-seq or Proteomics Data

Reference-Based Single-Cell RNA-Seq Annotation

Spatial Neighborhood Modeling and Differential Expression Analysis for Transcriptomics

Spatially-aware normalisation for spatial transcriptomics data

Spatial Interaction Markers

SpaceTrooper performs Quality Control analysis of Image-Based spatial

Spatial Transcriptomics Analysis

Identification and Classification of Spatial Artifacts in Visium and Visium HD Data

Cluster analysis of Spatial Transcriptomics data

Deconvolution of mixed cells from spatial and/or bulk gene expression data