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 …

Single-cell and single-nucleus RNA-sequencing technologies capture the expression of
plant genes at an unprecedented resolution. Therefore, these technologies are gaining …

The alevin-fry ecosystem provides a robust and growing suite of programs for single-cell
data processing. However, as new single-cell technologies are introduced, as the …

Abstract Background IL‐17A and TNF synergistically promote inflammation and
tumorigenesis. Their interplay and impact on ovarian carcinoma (OC) progression are …

We describe a workflow for preprocessing a wide variety of single-cell genomics data types.
The approach is based on parsing of machine-readable seqspec assay specifications to …

Next-generation sequencing libraries are constructed with numerous synthetic constructs
such as sequencing adapters, barcodes, and unique molecular identifiers. Such sequences …

Single-cell and single-nucleus genomics assays are becoming increasingly complex, with
multiple measurements of distinct modalities performed concurrently resulting in …

Results We present a tool called splitcode, that enables flexible and efficient parsing,
interpreting, and editing of sequencing reads. This versatile tool facilitates simple …

Cell atlas projects curate representative datasets, cell types, and marker genes for tissues
across an organism. Despite their ubiquity, atlas projects rely on duplicated and manual …