ma-compbio

Ma Lab at CMU's repositories

Hyper-SAGNN

hypergraph representation learning, graph neural network

Language:PythonMIT82 5 13

Higashi

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

Language:Jupyter NotebookMIT74 6 51

SpiceMix

spatial transcriptome, single cell

Language:Jupyter NotebookMIT60 3 4

MATCHA

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

Language:PythonMIT29 4 6

SNIPER

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

Language:PythonMIT29 4 7

Fast-Higashi

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

Language:Jupyter NotebookMIT17 4 5

Weaver

Allele-Specific Quantification of Structural Variations in Cancer Genomes

Language:C++MIT17 7 17

Phylo-HMRF

Language:PythonMIT15 8 14

scGHOST

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

Language:Jupyter NotebookMIT15 3 3

PEP

Language:PythonMIT14 4 2

GAGE-seq

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

Language:Jupyter NotebookMIT10 2 2

CTCF-MP

Language:PythonMIT9 50

DANGO

Language:PythonMIT7 30

UNADON

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

Language:PythonMIT7 5 1

MOCHI

Language:PythonMIT500

RACA

Language:PerlMIT500

MultiRes

Language:PythonMIT4 40

MutSpace

cancer mutation, mutation signature, sequence embedding

Language:PythonMIT3 40

Phylo-HMGP

Language:PythonMIT3 5 2

ChangeLocator

Language:Python200

DESCHRAMBLER

Language:PerlMIT200

SPIN

nuclear compartmentalization, 3D genome, nuclear bodies, MRF

Language:PythonMIT2 4 1

CONCERT

Language:PythonMIT1 40

Graphene

1 40

LDGM

Language:MATLABMIT100

MFRT

Language:Shell100

SpaceFormer

Language:Jupyter Notebook100

cnb

Language:GoNOASSERTION000

PSAR

Language:C++MIT000

PSAR-Align

Language:C++MIT000