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kallisto, bustools and kb-python for quantifying bulk, single-cell and single-nucleus RNA-seq
The term 'RNA-seq'refers to a collection of assays based on sequencing experiments that
involve quantifying RNA species from bulk tissue, single cells or single nuclei. The kallisto …
involve quantifying RNA species from bulk tissue, single cells or single nuclei. The kallisto …
Navigating bottlenecks and trade-offs in genomic data analysis
Genome sequencing and analysis allow researchers to decode the functional information
hidden in DNA sequences as well as to study cell to cell variation within a cell population …
hidden in DNA sequences as well as to study cell to cell variation within a cell population …
Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells
RNA velocity has been rapidly adopted to guide interpretation of transcriptional dynamics in
snapshot single-cell data; however, current approaches for estimating RNA velocity lack …
snapshot single-cell data; however, current approaches for estimating RNA velocity lack …
Recovery of missing single-cell RNA-sequencing data with optimized transcriptomic references
Single-cell RNA-sequencing (scRNA-seq) is an indispensable tool for characterizing cellular
diversity and generating hypotheses throughout biology. Droplet-based scRNA-seq datasets …
diversity and generating hypotheses throughout biology. Droplet-based scRNA-seq datasets …
Fulgor: a fast and compact k-mer index for large-scale matching and color queries
The problem of sequence identification or matching—determining the subset of reference
sequences from a given collection that are likely to contain a short, queried nucleotide …
sequences from a given collection that are likely to contain a short, queried nucleotide …
Single-cell omics: experimental workflow, data analyses and applications
Cells are the fundamental units of biological systems and exhibit unique development
trajectories and molecular features. Our exploration of how the genomes orchestrate the …
trajectories and molecular features. Our exploration of how the genomes orchestrate the …
Benchmarking UMI-based single-cell RNA-seq preprocessing workflows
Background Single-cell RNA-sequencing (scRNA-seq) technologies and associated
analysis methods have rapidly developed in recent years. This includes preprocessing …
analysis methods have rapidly developed in recent years. This includes preprocessing …
Next-generation forward genetic screens: uniting high-throughput perturbations with single-cell analysis
Programmable genome-engineering technologies, such as CRISPR (clustered regularly
interspaced short palindromic repeats) nucleases and massively parallel CRISPR screens …
interspaced short palindromic repeats) nucleases and massively parallel CRISPR screens …
[HTML][HTML] Recent advances in T-cell receptor repertoire analysis: bridging the gap with multimodal single-cell RNA sequencing
T cells exercise a multitude of functions such as cytotoxicity, secretion of immunomodulating
cytokines or regulation of tolerance, collectively resulting in an effective control of immune …
cytokines or regulation of tolerance, collectively resulting in an effective control of immune …
IL-1β-induced epithelial cell and fibroblast transdifferentiation promotes neutrophil recruitment in chronic rhinosinusitis with nasal polyps
X **e, P Wang, M **, Y Wang, L Qi, C Wu… - Nature …, 2024 - nature.com
Neutrophilic inflammation contributes to multiple chronic inflammatory airway diseases,
including asthma and chronic rhinosinusitis with nasal polyps (CRSwNP), and is associated …
including asthma and chronic rhinosinusitis with nasal polyps (CRSwNP), and is associated …