cellswith

Cellswith is a term encountered in biology and bioinformatics to denote a subset of cells that possess a specific attribute, such as expression of a marker, a functional state, or a phenotypic feature. It is not a formal scientific designation, but a label used in datasets, analysis scripts, and documentation to identify or annotate cells that meet a criterion.

In practice, cellswith often appears as a metadata tag or variable name in single-cell analysis workflows. For example, a dataset might include a boolean or categorical field 'cellswith_marker_X' describing cells that express marker X above a threshold. The label is frequently used alongside 'cellswithout' to mark cells that do not meet the criterion. It is common in tutorials, notebooks, and open-source software to illustrate filtering, subsetting, or downstream analysis steps.

To determine which cells are labeled 'cellswith', researchers apply analytic methods such as gene-expression thresholds, marker-scoring, or automated cell-annotation algorithms. The resulting subset is treated as a group for downstream comparisons or visualizations, but the 'cellswith' label itself is metadata rather than a distinct biological category.

The term lacks formal standardization and may be superseded by more precise descriptors such as 'cells expressing X' or 'Cell population A expressing marker Y'. Some software packages normalize labels to 'with' and 'without' columns in metadata tables; naming conventions vary by project.

See also: single-cell RNA sequencing, cell annotation, marker genes, metadata in bioinformatics, data labeling conventions.