Motivation Increasing numbers of large scale single cell RNA-Seq projects are leading to a
data explosion, which can only be fully exploited through data integration. A number of …

Motivation: Accurate alignment of high-throughput RNA-seq data is a challenging and yet
unsolved problem because of the non-contiguous transcript structure, relatively short read …

The growing number of available single-cell gene expression datasets from different species
creates opportunities to explore evolutionary relationships between cell types across …

Alignment of scRNA-Seq data are the first and one of the most critical steps of the scRNA-
Seq analysis workflow, and thus the choice of proper aligners is of paramount importance …

Motivation: The alignment of sequencing reads to a transcriptome is a common and
important step in many RNA-seq analysis tasks. When aligning RNA-seq reads directly to a …

Recent advances in single-cell technologies and integration algorithms make it possible to
construct comprehensive reference atlases encompassing many donors, studies, disease …

We present STARsolo, a comprehensive turnkey solution for quantifying gene expression in
single-cell/nucleus RNA-seq data, built into RNA-seq aligner STAR. Using simulated data …

High-throughput RNA sequencing is an increasingly accessible method for studying gene
structure and activity on a genome-wide scale. A critical step in RNA-seq data analysis is the …

Single-cell atlases often include samples that span locations, laboratories and conditions,
leading to complex, nested batch effects in data. Thus, joint analysis of atlas datasets …

Alignment is the first step in most RNA-seq analysis pipelines, and the accuracy of
downstream analyses depends heavily on it. Unlike most steps in the pipeline, alignment is …