kamath_2022_ctrl

Will Macnair - Computational Sciences Center of Excellence, F Hoffmann-La Roche Ltd, Basel, Switzerland

March 23, 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

  • da_neurons_0.2 (link)

Config files

▸ config-kamath_2022_ctrl.yaml (click to expand) 
project:
  proj_dir:         /pmount/projects/site/pred/brain-sc-data/kamath_2022_ctrl
  fastq_dir:        /pmount/projects/site/pred/brain-sc-analysis/studies/Kamath_2022_pos/data/fastqs
  full_tag:         kamath_2022_ctrl
  short_tag:        kamath
  your_name:        Will Macnair
  affiliation:      Computational Sciences Center of Excellence, F Hoffmann-La Roche Ltd, Basel, Switzerland
  sample_metadata:  data/metadata/sample_metadata_kamath_2022_ctrl_pos.csv
  ref_txome:        human_2024
  date_stamp:       "2026-03-23"
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_kamath_2022_ctrl_dopaminergic.yaml
resources:
  retries:              2
  gb_save_alevin_to_h5: 16
  gb_run_cellbender:    32
▸ zoom_params_kamath_2022_ctrl_dopaminergic.yaml (click to expand) 
zoom:
  name:           da_neurons
  labels_source:  clusters
  sel_labels:     [cl02]
  labels_col:     RNA_snn_res.0.2
qc:
  qc_min_cells:   50
integration:
  int_n_dims:     20