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Overview
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in silico cancer center
iscc
pedrofale/iscc
Home
Overview
Installation
Tutorials
Tutorials
iscc overview
Tumor evolution
Tumor evolution
Exploring the tumor
The shared tumour — one multi-focal DCIS→IDC lesion behind every science notebook
Compartment selection: DCIS → IDC and the genetic-vs-niche expression confound
Treatment and the four modes of therapeutic escape
Metastasis: DCIS → IDC → metastasis → treatment
Data generation
Data generation
DNA sequencing: bulk and single cell
scRNA-seq on a simulated tumour
Spatial transcriptomics: a Visium slide over a simulated tumour
DNA read emission: count/coverage matrix -> FASTQ / BAM
Data analysis examples
Data analysis examples
The analysis dataset and its ground truth
Calling copy number from single-cell DNA with HMMcopy
Tree reconstruction from single-cell DNA with SCITE
Clone inference from bulk DNA with PyClone-VI
Integrating scDNA and scRNA with clonealign
Calling copy number from scRNA with Numbat
Deconvolving Visium spots with RCTD
Recovering progression constraints with TreeMHN
Progression constraints from cross-sectional data with MHN
Integrating a patient cohort with scDEF
Cell–cell communication with CellChat
API Reference
API Reference
Tumor
Tumor
GenotypeTumor
GlandularTumor
Tumor (base)
Treatment
Treatment
Chemotherapy
TargetedTherapy
Immunotherapy
Surgery
Treatment (base)
Sample
Sample
Resection
Biopsy
Dissociation
spatialize
tissue_image
Data
Data
bulkDNA
scDNA
scRNA
Visium
DNA (base)
DNABatchHyperParams
RNABatchHyperParams
VisiumBatchHyperParams
Reads
Reads
emit_dna_reads
emit_scrna_reads
emit_visium_reads
Inference
Inference
ABC
Prior
Posterior
Calibration
Calibration
estimate_dna
estimate_rna
estimate_visium
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