scRNAseq analysis notes from Ming Tang

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Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection

Tutorial for scRNA-seq data analysis beginners using R

Single cell RNA sequencing analysis course

Single RNA-seq data analysis with R (Finland, May, 2019)

Clustering scRNAseq by genotypes

Bench-marking classification tools for scRNA-seq data

An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.

The need to understand cell developmental processes has spawned a plethora of computational methods for discovering hierarchies from scRNAseq data. However, existing techniques are based on Euclidean geometry which is not an optimal choice for modeling complex cell trajectories with multiple branches. To overcome this fundamental representation issue we propose Poincaré maps, a method harnessing the power of hyperbolic geometry into the realm of single-cell data analysis.

This repository contains R code, with which you can create 3D UMAP and tSNE plots of Seurat analyzed scRNAseq data

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Systematically learn and evaluate the latent geometry of high-dimensional data, with a focus on scRNAseq analysis

Single Cell Cluster Evaluation

scGSVA: Perform GSVA for single cell RNA seq

a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.

A Snakemake workflow and MrBiomics module for processing and visualizing (multimodal) sc/snRNA-seq data generated with 10X Genomics Kits or in the MTX matrix file format powered by the R package Seurat.

Cell type pipes for R

Explore and share your scRNAseq clustering results

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Workflow for single-cell RNA-seq analysis using Seurat

Scripts to run and benchmark scRNA-seq cell cluster labeling methods

A study to compare methods for clustering of scRNA-seq data

Experimental design framework for scRNAseq population studies (eQTL and DE)

🦠 Regularly updated list of publicly available datasets with single-cell (scRNAseq) and T-cell/antibody immune repertoire (AIRR / RepSeq / immunosequencing) data of COVID-19 patients with SARS-CoV-2.

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Repository for the building, sharing and editing of scRNAseq pipelines for the Lung Cell Atlas

scRNAseq integration with triplet neural networks

Harvard FAS informatics scRNAseq workshop website

Wasserstein Generative Adversarial Network for analysing scRNAseq data