High dimensional weighted gene co-expression network analysis

Benchmarking analysis of data integration tools

Assessing the purity of single cell population

DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map the cell transcriptome as a function of its environment.

A novel manifold learning approach to reveal the functional links between gene networks

An interactive explorer for single-cell transcriptomics data

A Bayesian model for compositional single-cell data analysis

Epigenetic regulator function through mouse gastrulation

An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

WDL Analysis Research Pipelines

A list of scRNA-seq analysis tools

Granular Functional Filtering (Gruffi) to isolate stressed cells

R package for specialised analysis of single cell data

Clustering scRNAseq by genotypes

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

R package for detecting doublets in single-cell RNA sequencing data

Helper tools for popscle

Demultiplexing pooled scRNA-seq data with or without genotype reference

Genetic multiplexing of barcoded single cell RNA-seq

The fastai book, published as Jupyter Notebooks

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to represent new studies without additional training.

Reference mapping for single-cell genomics

Make Complex Heatmaps