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Integrated multi-omics approaches to improve classification of chronic kidney disease
Chronic kidney diseases (CKDs) are currently classified according to their clinical features,
associated comorbidities and pattern of injury on biopsy. Even within a given classification …
associated comorbidities and pattern of injury on biopsy. Even within a given classification …
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 …
Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data
The rapid growth of high-throughput single-cell and single-nucleus RNA-sequencing
(scRNA-seq and snRNA-seq) technologies has produced a wealth of data over the past few …
(scRNA-seq and snRNA-seq) technologies has produced a wealth of data over the past few …
SoloTE for improved analysis of transposable elements in single-cell RNA-Seq data using locus-specific expression
R Rodríguez-Quiroz… - Communications …, 2022 - nature.com
Abstract Transposable Elements (TEs) contribute to the repetitive fraction in almost every
eukaryotic genome known to date, and their transcriptional activation can influence the …
eukaryotic genome known to date, and their transcriptional activation can influence the …
Simulation, power evaluation and sample size recommendation for single-cell RNA-seq
Motivation Determining the sample size for adequate power to detect statistical significance
is a crucial step at the design stage for high-throughput experiments. Even though a number …
is a crucial step at the design stage for high-throughput experiments. Even though a number …
A Bayesian framework for inter-cellular information sharing improves dscRNA-seq quantification
Motivation Droplet-based single-cell RNA-seq (dscRNA-seq) data are being generated at an
unprecedented pace, and the accurate estimation of gene-level abundances for each cell is …
unprecedented pace, and the accurate estimation of gene-level abundances for each cell is …
Fast and accurate matching of cellular barcodes across short-reads and long-reads of single-cell RNA-seq experiments
Single-cell RNA sequencing allows for characterizing the gene expression landscape at the
cell type level. However, because of its use of short-reads, it is severely limited at detecting …
cell type level. However, because of its use of short-reads, it is severely limited at detecting …
TKSM: highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator
Motivation Transcriptomic long-read (LR) sequencing is an increasingly cost-effective
technology for probing various RNA features. Numerous tools have been developed to …
technology for probing various RNA features. Numerous tools have been developed to …
scReadSim: a single-cell RNA-seq and ATAC-seq read simulator
Benchmarking single-cell RNA-seq (scRNA-seq) and single-cell Assay for Transposase-
Accessible Chromatin using sequencing (scATAC-seq) computational tools demands …
Accessible Chromatin using sequencing (scATAC-seq) computational tools demands …
SimCH: simulation of single-cell RNA sequencing data by modeling cellular heterogeneity at gene expression level
Single-cell ribonucleic acid (RNA) sequencing (scRNA-seq) has been a powerful
technology for transcriptome analysis. However, the systematic validation of diverse …
technology for transcriptome analysis. However, the systematic validation of diverse …