Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods
Single-cell transcriptomics can profile thousands of cells in a single experiment and identify
novel cell types, states and dynamics in a wide variety of tissues and organisms. Standard …
novel cell types, states and dynamics in a wide variety of tissues and organisms. Standard …
[HTML][HTML] Automated methods for cell type annotation on scRNA-seq data
G Pasquini, JER Arias, P Schäfer… - Computational and …, 2021 - Elsevier
The advent of single-cell sequencing started a new era of transcriptomic and genomic
research, advancing our knowledge of the cellular heterogeneity and dynamics. Cell type …
research, advancing our knowledge of the cellular heterogeneity and dynamics. Cell type …
[HTML][HTML] muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data
Single-cell RNA sequencing (scRNA-seq) has become an empowering technology to profile
the transcriptomes of individual cells on a large scale. Early analyses of differential …
the transcriptomes of individual cells on a large scale. Early analyses of differential …
Profiling cell type abundance and expression in bulk tissues with CIBERSORTx
CB Steen, CL Liu, AA Alizadeh… - Stem Cell Transcriptional …, 2020 - Springer
CIBERSORTx is a suite of machine learning tools for the assessment of cellular abundance
and cell type-specific gene expression patterns from bulk tissue transcriptome profiles. With …
and cell type-specific gene expression patterns from bulk tissue transcriptome profiles. With …
[HTML][HTML] A comparison of automatic cell identification methods for single-cell RNA sequencing data
Background Single-cell transcriptomics is rapidly advancing our understanding of the
cellular composition of complex tissues and organisms. A major limitation in most analysis …
cellular composition of complex tissues and organisms. A major limitation in most analysis …
[HTML][HTML] Microglial amyloid beta clearance is driven by PIEZO1 channels
H Jäntti, V Sitnikova, Y Ishchenko… - Journal of …, 2022 - Springer
Background Microglia are the endogenous immune cells of the brain and act as sensors of
pathology to maintain brain homeostasis and eliminate potential threats. In Alzheimer's …
pathology to maintain brain homeostasis and eliminate potential threats. In Alzheimer's …
[HTML][HTML] Challenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single-cell RNA-sequencing datasets
Deconvolution of cell mixtures in “bulk” transcriptomic samples from homogenate human
tissue is important for understanding disease pathologies. However, several experimental …
tissue is important for understanding disease pathologies. However, several experimental …
scClassify: sample size estimation and multiscale classification of cells using single and multiple reference
Automated cell type identification is a key computational challenge in single‐cell RNA‐
sequencing (sc RNA‐seq) data. To capitalise on the large collection of well‐annotated sc …
sequencing (sc RNA‐seq) data. To capitalise on the large collection of well‐annotated sc …
A comprehensive comparison of supervised and unsupervised methods for cell type identification in single-cell RNA-seq
The cell type identification is among the most important tasks in single-cell RNA-sequencing
(scRNA-seq) analysis. Many in silico methods have been developed and can be roughly …
(scRNA-seq) analysis. Many in silico methods have been developed and can be roughly …
[HTML][HTML] Decreased left heart flow in fetal lambs causes left heart hypoplasia and pro-fibrotic tissue remodeling
MS Reuter, DJ Sokolowski, J Javier Diaz-Mejia… - Communications …, 2023 - nature.com
Low blood flow through the fetal left heart is often conjectured as an etiology for hypoplastic
left heart syndrome (HLHS). To investigate if a decrease in left heart flow results in growth …
left heart syndrome (HLHS). To investigate if a decrease in left heart flow results in growth …