Source: https://docs.nygen.io/CyteArc/api/perturbation.html
Revision: eed5a4b181a88db28ff2085b3494f24aa173373d

Perturbation API reference
**************************

Pooled single-cell CRISPR screens, such as Perturb-seq, CROP-seq,
ECCITE-seq and 10x CRISPR Guide Capture, give each cell guide RNAs
that switch one target gene off or on, and capture the guides beside
the transcriptome. CyteArc imports the guide counts as an assay
declared "CRISPR". Guide calling decides which guides each cell
carries, since every cell also holds a few ambient guide molecules;
"cytearc.perturbation" holds the record of those calls.

The steps run on a "DataStore". "ds.perturbation.import_guide_calls"
saves Cell Ranger’s calls from "protospacer_calls_per_cell.csv" as a
"guide_calls" artifact, "ds.perturbation.load_guide_calls" reads that
artifact as a "GuideCalls" record, and "ds.plots.guide_calls" plots
how many guides each cell carries and how many cells carry each guide.

A "guide_calls" artifact labels each cell with its one called guide,
with ""Negative"" when no guide is called, and with ""Multiple"" when
several are. The labels group cells like cluster labels do, so
"ds.select_cells(calls, include=["GUIDE-1"])" selects the cells of one
guide and plots colour cells by their call; "ds.select_cells(calls,
value="n_guides", low=1, high=1, keep_bounds=True)" keeps the cells
with exactly one called guide. Read per-cell values lists the
artifact’s arrays.


Guide calls
===========

class cytearc.perturbation.GuideCalls(cells, calls, guides, source)

   The guide calls of a set of cells, read from a "guide_calls"
   artifact.

   cells

      One row per cell, indexed by cell "ids", with "call" (the ID of
      a cell’s one called guide, ""Negative"", or ""Multiple""),
      "n_guides", "top_guide" (an empty string for a cell with no
      guide UMIs), "top_umi", "top_fraction" (NaN for a cell with no
      guide UMIs) and "total_umi".

   calls

      One row per called guide of a cell, with the cell’s "ids", the
      "guide" and its "umis", most UMIs first within each cell.

   guides

      The ID of every guide of the assay, in assay order, including
      guides called in no cell.

   source

      The operation that made the calls: ""import_guide_calls"" for
      Cell Ranger’s calls.