Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells
Sophisticated methods to properly pre-process and analyze the increasing collection of single-cell RNA sequencing (scRNA-seq)…
Browsing: Cell Type Analysis
CellMap – in silico cell type decomposition is an efficient, inexpensive, and convenient alternative to scRNA-Seq that can leverage bulk RNA-seq
Induced pluripotent stem cell (iPSC) derived cell types are increasingly employed as in vitro model…
Machine learning for cell type classification from single nucleus RNA sequencing data
With the advent of single cell/nucleus RNA sequencing (sc/snRNA-seq), the field of cell phenotyping is…
totRNAseq – high-throughput muscle fiber typing from RNA sequencing data
Skeletal muscle fiber type distribution has implications for human health, muscle function, and performance. This…
Kassandra – precise reconstruction of the TME using bulk RNA-seq and a machine learning algorithm trained on artificial transcriptomes
Cellular deconvolution algorithms virtually reconstruct tissue composition by analyzing the gene expression of complex tissues.…
STRIDE – a topic-model-based method to deconvolve spatial transcriptomics using scRNA-seq
The recent advances in spatial transcriptomics have brought unprecedented opportunities to understand the cellular heterogeneity…
Gruffi – an algorithm for improved delineation of developmental trajectories in organoids and resemblance to in vivo data.
Organoids enable in vitro modeling of complex developmental processes and disease pathologies. Like most 3D cultures, organoids…
Benchmarking methods for detecting differential states between conditions from multi-subject single-cell RNA-seq data
Single-cell RNA-sequencing (scRNA-seq) enables researchers to quantify transcriptomes of thousands of cells simultaneously and study…
ActiveSVM – single-cell mRNA-seq data analysis with a minimal number of genes
Sequencing costs currently prohibit the application of single-cell mRNA-seq to many biological and clinical analyses.…
DestVI – identification of continuums of cell types in spatial transcriptomics data
Most spatial transcriptomics technologies are limited by their resolution, with spot sizes larger than that…