Discover ma-compbio/GAGE-seq Open Source project

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10
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Jupyter Notebook
License
MIT License
Created about 1 year ago
Updated 6 months ago

ma-compbio

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Data processing and analysis workflow for GAGE-seq, a coassay of single-cell HiC and single-cell RNA-seq

Hyper-SAGNN

hypergraph representation learning, graph neural network

Python

Higashi

single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph

Jupyter Notebook

SpiceMix

spatial transcriptome, single cell

Jupyter Notebook

SNIPER

nuclear compartments, subcompartments, nuclear organization, Hi-C, autoencoder

Python

MATCHA

multiway chromatin interaction, 3D genome, single-nucleus, hypergraph representation learning

Python

Weaver

Allele-Specific Quantification of Structural Variations in Cancer Genomes

C++

Fast-Higashi

single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, tensor decomposition

Jupyter Notebook

scGHOST

single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, genome subcompartment

Phylo-HMRF

PEP

SPEID

CTCF-MP

UNADON

Transformer-based model to predict genome-wide chromosome spatial position

DANGO

MOCHI

RACA

MultiRes

MutSpace

cancer mutation, mutation signature, sequence embedding

Phylo-HMGP

DESCHRAMBLER

ChangeLocator

SPIN

nuclear compartmentalization, 3D genome, nuclear bodies, MRF

Python

MFRT

Shell

Graphene

LDGM

CONCERT

SpaceFormer

TSA-Seq-toolkit

ma-compbio/GAGE-seq

ma-compbio

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