High-level wrapper that computes QC metrics, flags low-quality cells, (optionally) detects doublets and performs lightweight annotation, and renders an HTML report.

Usage

run_qc_pipeline(
  obj,
  species = c("mouse", "human"),
  method = c("gmm", "threshold", "auto"),
  score_cutoff = 2,
  auto_k = 3,
  assay = "RNA",
  save_dir = "qc_outputs",
  report_file = "qc_report.html",
  spliced = NULL,
  unspliced = NULL,
  spliced_obj = NULL,
  spliced_assay = NULL,
  spliced_layer = "counts",
  unspliced_obj = NULL,
  unspliced_assay = NULL,
  unspliced_layer = "counts",
  doublets = c("none", "auto", "doubletfinder", "scdblfinder"),
  remove_doublets = TRUE,
  sample_col = NULL,
  annot_method = c("marker_score", "singleR", "sctype", "none"),
  marker_source = c("panglao", "internal", "custom"),
  panglao_file = NULL,
  canonical_only = TRUE,
  ui_max = 0.2,
  tissue = NULL,
  min_genes = 5,
  report_html = TRUE,
  theme_bootswatch = "minty",
  debug = FALSE,
  sctype_db_path = system.file("extdata", "ScTypeDB_full.xlsx", package = "scQCenrich",
    mustWork = FALSE),
  marker_method = c("findmarkers", "module_score"),
  annot_args = NULL,
  unknown_min_genes = 2,
  unknown_min_margin = 0.01,
  unknown_min_top = 0.01,
  qc_strength = c("auto", "default", "lenient", "strict"),
  rescue_mode = c("moderate", "lenient", "strict", "none"),
  cancer_bypass = FALSE,
  enrichment_plots = TRUE
)

Arguments

obj

Seurat object

species

'mouse' or 'human'

method

'threshold', 'gmm' or 'auto'

score_cutoff

Integer cutoff used by 'threshold' mode

auto_k

Ignored; kept for back-compat

assay

Assay name

save_dir

Directory for intermediate outputs

report_file

Output HTML report path

spliced, unspliced

Back-compat layer strings on the same object

spliced_obj, unspliced_obj

Optional external Seurat objects

spliced_assay, unspliced_assay

Assay names on external objects

spliced_layer, unspliced_layer

Layer/slot on external objects

doublets

'auto','doubletfinder','scdblfinder','none'

remove_doublets

Logical; if TRUE, mark doublets to remove/borderline

sample_col

Optional meta column with sample/group

annot_method

'SingleR','marker_score','none'

marker_source

'panglao', 'internal', 'custom' (only used when annot_method='marker_score')

panglao_file

Optional path to Panglao TSV (defaults to inst/extdata if present)

canonical_only, ui_max, min_genes

Panglao signature filtering knobs

tissue

Character vector of organ/tissue names used to subset the PanglaoDB marker database before cell-type scoring (annot_method = "marker_score" only). Supplying the correct tissue greatly improves annotation accuracy by restricting signatures to cell types that are actually present in your sample. Pass NULL (default) to use all tissues.

Supported tissue names (case-insensitive, exact match preferred): "Adrenal glands", "Blood", "Bone", "Brain", "Connective tissue", "Embryo", "Epithelium", "Eye", "GI tract", "Heart", "Immune system", "Kidney", "Liver", "Lungs", "Mammary gland", "Olfactory system", "Oral cavity", "Pancreas", "Parathyroid glands", "Placenta", "Reproductive", "Skeletal muscle", "Skin", "Smooth muscle", "Thymus", "Thyroid", "Urinary bladder", "Vasculature", "Zygote".

Example — PBMC / whole blood: tissue = c("Blood", "Immune system"). Example — heart: tissue = "Heart".

report_html

Logical; if TRUE, render the report

theme_bootswatch

Bootswatch theme for report

debug

Logical for verbose messages

sctype_db_path

Path to ScType Excel DB. Defaults to the packaged file

marker_method

Either "module_score" (default) or "findmarkers".

annot_args

List of extra args forwarded to auto_annotate().

unknown_min_genes

Integer; guard for "unknown" assignment.

unknown_min_margin

Numeric; guard for "unknown" assignment.

unknown_min_top

Integer; guard for "unknown" assignment.

qc_strength

One of c("auto","default","lenient","strict"); passed to flagLowQuality().

rescue_mode

One of c("moderate","lenient","strict","none"); controls how aggressively borderline cells are rescued. Default "moderate".

cancer_bypass

Logical. If TRUE, clusters with healthy splicing profiles but high removal rates are exempt from the removal-fraction penalty (useful for cancer datasets). Default FALSE.

enrichment_plots

logical. If TRUE, run GO/KEGG enrichment plots; if FALSE, skip. Default: TRUE.

Value

A list with at least: $obj (QC-kept), $metrics, $status_df, $report_file. Also returns $obj_all for convenience.