NicheNet: predict active ligand-target links between interacting cells

A repository for setting up a RNAseq workflow

Table of software for the analysis of single-cell RNA-seq data.

Differential analysis of RNA-Seq

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

Reference-guided transcript discovery and quantification for long read RNA-Seq data

Color blindness friendly visualization of single-cell and bulk RNA-sequencing data

Batch effect adjustment based on negative binomial regression for RNA sequencing count data

Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data

Cell type annotation with local Large Language Models (LLMs) - Ensuring privacy and speed with extensive customized reports

Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project

Visual self-service analytics platform for big omics data.

Infer cell types in scRNA-seq data using bulk RNA-seq or gene sets

Statistical Analysis of RNA-Seq Tools

integrated RNA-seq Analysis Pipeline

SIB course on single cell transcriptomics by mostly using the Seurat pipeline

Repository for the R package EPIC, to Estimate the Proportion of Immune and Cancer cells from bulk gene expression data.

Transcriptomics Visualization R package.