SRTsim – spatial pattern preserving simulations for spatially resolved transcriptomics
Spatially resolved transcriptomics (SRT)-specific computational methods are often developed, tested, validated, and evaluated in silico…
Browsing: Publications
SpliceTools – a suite of downstream RNA splicing analysis tools to investigate mechanisms and impact of alternative splicing
As a fundamental aspect of normal cell signaling and disease states, there is great interest…
Yale team co-maps proteins and transcriptome in human tissues with spatial CITE-seq
To understand how cells behave, researchers also need to understand the molecules that make them…
scPrisma – inference of topological signals in single-cell data using spectral template matching
Single-cell RNA sequencing has been instrumental in uncovering cellular spatiotemporal context. This task is challenging…
GraphST – spatially informed clustering, integration, and deconvolution of spatial transcriptomics
Spatial transcriptomics technologies generate gene expression profiles with spatial context, requiring spatially informed analysis tools…
IBRAP – integrated benchmarking single-cell RNA-sequencing analytical pipeline
Single-cell ribonucleic acid (RNA)-sequencing (scRNA-seq) is a powerful tool to study cellular heterogeneity. The high…
MATQ_Drop – Multiple-Annealing-and-Tailing-based Quantitative scRNA-seq in Droplets
Synapses are crucial structures that mediate signal transmission between neurons in complex neural circuits and…
Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously
Large compendia of gene expression data have proven valuable for the discovery of novel biological…
scSTAR – single-cell State Transition Across-samples of RNA-seq data
Cell-state transition can reveal additional information from single-cell ribonucleic acid (RNA)-sequencing data in time-resolved biological…
mtscATAC-seq – mitochondrial single-cell assay for transposase-accessible chromatin with sequencing
Natural sequence variation within mitochondrial DNA (mtDNA) contributes to human phenotypes and may serve as…