SURGE – uncovering context-specific genetic-regulation of gene expression from single-cell RNA sequencing using latent-factor models
Genetic regulation of gene expression is a complex process, with genetic effects known to vary…
Browsing: Analysis Pipelines
scFed – federated learning for cell type classification with scRNA-seq
The advent of single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of cellular heterogeneity and…
Cellograph – a semi-supervised approach to analyzing multi-condition single-cell RNA-sequencing data using graph neural networks
With the growing number of single-cell datasets collected under more complex experimental conditions, there is…
STIGMA – Single-cell tissue-specific gene prioritization using machine learning
Clinical exome and genome sequencing have revolutionized the understanding of human disease genetics. Yet many…
scSNV-seq – high-throughput phenotyping of single nucleotide variants by coupled single-cell genotyping and transcriptomics
CRISPR screens with single-cell transcriptomic readouts are a valuable tool to understand the effect of…
SinCMat – A single-cell-based method for predicting functional maturation transcription factors
A major goal of regenerative medicine is to generate tissue-specific mature and functional cells. However,…
scBayes – a Bayesian framework to study tumor subclone–specific expression by combining bulk DNA and single-cell RNA sequencing data
Genetic and gene expression heterogeneity is an essential hallmark of many tumors, allowing the cancer…
Advancing single-cell RNA-seq data analysis through the fusion of multi-layer perceptron and graph neural network
The advancement of single-cell sequencing technology has smoothed the ability to do biological studies at…
RENGE infers gene regulatory networks using time-series single-cell RNA-seq data with CRISPR perturbations
Single-cell RNA-seq analysis coupled with CRISPR-based perturbation has enabled the inference of gene regulatory networks…
A guide to single-cell RNA sequencing analysis using web-based tools for non-bioinformatician
Single-cell RNA sequencing (scRNA-seq) is a technique that has proven to be a powerful tool…