pineda_2024

Will Macnair - Neuroscience and Rare Diseases, Roche Innovation Center, Basel, Switzerland

February 28, 2026

This page serves as a starting point for exploring the results of scprocess. The links below organize all generated reports, with each one detailing a specific step of the analysis (e.g., mapping, ambient RNA removal, QC).

Use this page to navigate through the full set of visualizations and outputs for your project.

Core steps

  • Mapping (link)

  • Ambient RNA removal (link)

  • QC (link)

  • Highly variable genes (link)

  • Integration (link)

  • Marker genes (link)

Cell type annotation

  • Celltype labelling (link)

Subclustering

Config files

▸ config-pineda_2024.yaml (click to expand) 
project:
  proj_dir:         /pstore/data/brain-sc-analysis/studies/pineda_2024
  arv_uuids:        [not shown]
  arv_instance:     arkau
  show_arv_uuids:   False
  full_tag:         pineda_2024
  short_tag:        pineda
  your_name:        Will Macnair
  affiliation:      Neuroscience and Rare Diseases, Roche Innovation Center, Basel, Switzerland
  sample_metadata:  data/metadata/pineda_2024_harmonized_metadata.csv
  metadata_vars:    [diagnosis, diagnosis_subtype, original_tissue_annotation]
  ref_txome:        human_2024
  date_stamp:       "2026-02-28"
  custom_sample_params: data/metadata/custom_params_pineda_2024.yaml
  # exclude:
  #   sample_id:      [SRR27882190]
ambient:
  ambient_method:   cellbender
qc:
  qc_max_mito:      0.10
  qc_max_splice:    0.75
marker_genes:
  mkr_custom_genesets:
  - name: human_brain
label_celltypes:
  - labeller:       scprocess
    model:          human_cns
zoom:
  - data/metadata/zoom_params_pineda_2024_myeloid.yaml
  - data/metadata/zoom_params_pineda_2024_neurons.yaml
resources:
  retries:                          1
  gb_render_html_label_celltypes:   32
  gb_render_html_zoom:              32
  gb_run_integration:               64
  gb_run_marker_genes:              98
  gb_zoom_run_marker_genes:         98
  mins_render_html_label_celltypes: 60
  mins_run_cellbender:              180
  mins_run_mapping:                 120
  mins_run_marker_genes:            180
  mins_zoom_run_marker_genes:       120
▸ custom_params_pineda_2024.yaml (click to expand) 
sample_id:
  SRR27882190:
    ambient:
      cb_expected_cells:           4197
      cb_total_droplets_included: 85000
      cb_low_count_threshold:        50
▸ zoom_params_pineda_2024_myeloid.yaml (click to expand) 
zoom:
  name:           myeloid
  labels_source:  scprocess
  model:          human_cns
  sel_labels:     ["Micro_Mono"]
  labels_col:     predicted_label_agg
integration:
  int_n_dims:     20
marker_genes:
  mkr_sel_res:    0.5
▸ zoom_params_pineda_2024_neurons.yaml (click to expand) 
zoom:
  name:           neurons
  labels_source:  scprocess
  model:          human_cns
  sel_labels:     ["Neurons"]
  labels_col:     predicted_label_agg