lasersonlab/scsearch

Index and search single cell data.

scsearch's Issues

Support hi/lo gene search

So far we have a simple search where genes are on or off, and for this we can index the sparse gene expression matrix. To do more sophisticated search where genes are hi/lo, we need the normalized matrix, and a more elaborate indexing scheme.

E.g. refering to http://stm.sciencemag.org/content/10/461/eaau4711

We first defined a flow cytometric strategy to identify the known B cell subsets and plasma cells in intestinal mucosa and in circulation, identifying plasma cells as live CD45⁺CD38^hiCD27⁺ cells and nonplasma cell B cells as live CD45⁺CD38⁻CD19⁺ cells. Among nonplasma cell B cells, naïve B cells were defined as CD45⁺CD38⁻CD19⁺IgD⁺IgM⁺ cells, whereas switched memory (SM) B cells were defined as CD45⁺CD38⁻CD19⁺IgD⁻IgM⁻ cells (fig. S2).

So [CD45⁺CD38⁻CD19⁺] would be a possible search query.