CLI reference

citeqc has four subcommands:

Command	Does
citeqc couple	measure protein~mRNA coupling per antibody and write a CSV
citeqc diagnose	run the diagnostics whose inputs you pass; exit code 1 if any flags
citeqc map	search the bundled antibody-to-gene table
citeqc example	write the synthetic example dataset as CSV files

Input tables are CSV (or TSV for .tsv/.txt; .gz and other compression is detected) with the row labels in the first column. For couple, adt, rna and meta have cells in rows; pass --transpose if adt and rna are features x cells. meta needs the stratum columns and the raw library sizes nCount_ADT and nCount_RNA.

For diagnose:

Option	Table
--adt + --meta	as for couple; missing antibodies must be empty (NaN), not 0
--stat	markers in rows, one column: your per-marker statistic
--groups	groups in rows, features in columns, plus a size column (--size-col, default n_cells)
--pvalues	one column of p-values
--bounded	features x samples, values in [0, 1]

The help text below is generated from the code when the site is built.

citeqc

usage: citeqc [-h] [--version] {couple,diagnose,map,example} ...

Protein~mRNA coupling and artefact diagnostics for CITE-seq data.

positional arguments:
  {couple,diagnose,map,example}
    couple              measure protein~mRNA coupling per antibody
    diagnose            run artefact checks
    map                 inspect the antibody->gene table
    example             write the synthetic example dataset as CSV files

options:
  -h, --help            show this help message and exit
  --version             show program's version number and exit

citeqc couple

usage: citeqc couple [-h] --adt ADT --rna RNA --meta META [--out OUT]
                     [--strata STRATA [STRATA ...]] [--group-size GROUP_SIZE]
                     [--draws DRAWS] [--min-groups MIN_GROUPS] [--seed SEED]
                     [--show SHOW] [--transpose] [--normalise]

options:
  -h, --help            show this help message and exit
  --adt ADT             cells x antibodies
  --rna RNA             cells x genes
  --meta META           cells x metadata (strata + nCount_ADT + nCount_RNA)
  --out OUT             output CSV (default: coupling.csv)
  --strata STRATA [STRATA ...]
                        metadata columns defining homogeneous strata (default:
                        ['donor', 'celltype'])
  --group-size GROUP_SIZE
                        cells per pseudo-group (default: 10)
  --draws DRAWS         random pseudo-group partitions per stratum (default: 10)
  --min-groups MIN_GROUPS
                        pseudo-groups a stratum must yield to be used (default: 25)
  --seed SEED           random seed (default: 0)
  --show SHOW           rows to print from each end
  --transpose           inputs are features x cells
  --normalise           inputs are raw counts: apply CLR (ADT) and log-CP10K (RNA,
                        scaled by meta's nCount_RNA)

citeqc diagnose

usage: citeqc diagnose [-h] [--adt ADT] [--meta META] [--by BY] [--transpose]
                       [--stat STAT] [--controls CONTROLS [CONTROLS ...]]
                       [--groups GROUPS] [--size-col SIZE_COL] [--pvalues PVALUES]
                       [--bounded BOUNDED]

options:
  -h, --help            show this help message and exit
  --adt ADT             cells x antibodies, for panel_consistency (needs --meta)
  --meta META           cells x metadata, for panel_consistency (needs --adt)
  --by BY               panel-consistency grouping column (default: donor)
  --transpose           --adt is antibodies x cells
  --stat STAT           one-column table: per-marker test statistic
  --controls CONTROLS [CONTROLS ...]
                        markers absent from the cells analysed
  --groups GROUPS       groups x features, plus a size column
  --size-col SIZE_COL   column of --groups holding cells per group (default: n_cells)
  --pvalues PVALUES     one-column table of p-values
  --bounded BOUNDED     bounded values (PSI/fractions), features x samples

citeqc map

usage: citeqc map [-h] [--query QUERY]
                  [--mechanism {splice_isoform,vesicular,IRE_3UTR}]

options:
  -h, --help            show this help message and exit
  --query QUERY         substring of antibody or gene
  --mechanism {splice_isoform,vesicular,IRE_3UTR}

citeqc example

usage: citeqc example [-h] [--seed SEED] [directory]

positional arguments:
  directory    output directory (default: citeqc_example)

options:
  -h, --help   show this help message and exit
  --seed SEED  random seed (default: 0)