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raphael-group

raphael-group

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paste

Probabilistic Alignment of Spatial Transcriptomics Experiments

Language:PythonLicense:BSD-3-ClauseStargazers:73Issues:10Issues:26

hatchet

HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, and that leverages the relationships between clones in these samples.

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chisel

CHISEL -- Copy-number Haplotype Inference in Single-cell by Evolutionary Links

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paste2

Probabilistic Alignment of Spatial Transcriptomics Experiments v.2

Language:Jupyter NotebookLicense:BSD-3-ClauseStargazers:25Issues:9Issues:6

decifer

DeCiFer is an algorithm that simultaneously selects mutation multiplicities and clusters SNVs by their corresponding descendant cell fractions (DCF).

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calder

CALDER (Cancer Analysis of Longitudinal Data through Evolutionary Reconstruction) reconstructs evolutionary trees from longitudinal bulk DNA sequencing data

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GASTON

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ConDoR

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scarlet

SCARLET (Single-cell Algorithm for Reconstructing Loss-supported Evolution of Tumors) is an algorithm that reconstructs tumor phylogenies from single-cell DNA sequencing data. SCARLET uses a loss-supported model that constrains mutation losses based on observed copy-number data.

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CalicoST

Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics

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fastBE

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belayer

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startle

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DeST_OT

Developmental Spatiotemporal Optimal Transport

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dialect

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copulacci

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LAML

LAML is a maximum likelihood algorithm to infer cell phylogeny from dynamic lineage tracing data

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lazac-copy-number

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superdendrix

SuperDendrix, an algorithm for identifying differential dependencies and associated genomic features.

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raphael-group.github.io

Raphael group website.

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CARTA

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hatchet2-paper

Publication repository for results that accompany the HATCHet2 paper.

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hatchet2-simulations

Snakemake pipeline for generating and running on new simulated data for HATCHet2 revisions

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hetdetect

Inferring Het SNP positions from tumor samples using Hidden Markov Models

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intmemoir-processed-data

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lab-tutorials

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laml-experiments

experiments for the LAML paper

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MERLIN

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MOLLUSC

Maximum Likelihood Estimation Of Lineage and Location Using Single Cell Spatial Lineage tracing Data

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sc-mail-experiments

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