Current best practices in single‐cell RNA‐seq analysis: a tutorial
Single‐cell RNA‐seq has enabled gene expression to be studied at an unprecedented
resolution. The promise of this technology is attracting a growing user base for single‐cell …
resolution. The promise of this technology is attracting a growing user base for single‐cell …
Eleven grand challenges in single-cell data science
The recent boom in microfluidics and combinatorial indexing strategies, combined with low
sequencing costs, has empowered single-cell sequencing technology. Thousands—or even …
sequencing costs, has empowered single-cell sequencing technology. Thousands—or even …
Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution
Spatial transcriptomics approaches have substantially advanced our capacity to detect the
spatial distribution of RNA transcripts in tissues, yet it remains challenging to characterize …
spatial distribution of RNA transcripts in tissues, yet it remains challenging to characterize …
DoubletFinder: doublet detection in single-cell RNA sequencing data using artificial nearest neighbors
Single-cell RNA sequencing (scRNA-seq) data are commonly affected by technical artifacts
known as" doublets," which limit cell throughput and lead to spurious biological conclusions …
known as" doublets," which limit cell throughput and lead to spurious biological conclusions …
[HTML][HTML] Transcriptional programs of neoantigen-specific TIL in anti-PD-1-treated lung cancers
Abstract PD-1 blockade unleashes CD8 T cells, including those specific for mutation-
associated neoantigens (MANA), but factors in the tumour microenvironment can inhibit …
associated neoantigens (MANA), but factors in the tumour microenvironment can inhibit …
Single-cell RNA-seq technologies and related computational data analysis
G Chen, B Ning, T Shi - Frontiers in genetics, 2019 - frontiersin.org
Single-cell RNA sequencing (scRNA-seq) technologies allow the dissection of gene
expression at single-cell resolution, which greatly revolutionizes transcriptomic studies. A …
expression at single-cell resolution, which greatly revolutionizes transcriptomic studies. A …
[HTML][HTML] Metabolic modeling of single Th17 cells reveals regulators of autoimmunity
Metabolism is a major regulator of immune cell function, but it remains difficult to study the
metabolic status of individual cells. Here, we present Compass, an algorithm to characterize …
metabolic status of individual cells. Here, we present Compass, an algorithm to characterize …
Chemoresistance evolution in triple-negative breast cancer delineated by single-cell sequencing
Triple-negative breast cancer (TNBC) is an aggressive subtype that frequently develops
resistance to chemotherapy. An unresolved question is whether resistance is caused by the …
resistance to chemotherapy. An unresolved question is whether resistance is caused by the …
Orchestrating single-cell analysis with Bioconductor
Recent technological advancements have enabled the profiling of a large number of
genome-wide features in individual cells. However, single-cell data present unique …
genome-wide features in individual cells. However, single-cell data present unique …
Single-cell RNA-seq denoising using a deep count autoencoder
Single-cell RNA sequencing (scRNA-seq) has enabled researchers to study gene
expression at a cellular resolution. However, noise due to amplification and dropout may …
expression at a cellular resolution. However, noise due to amplification and dropout may …