Ma Lab at CMU (@ma-compbio)
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ma-compbio

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Top repositories

1

Hyper-SAGNN

hypergraph representation learning, graph neural network
Python
82
star
2

Higashi

single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph
Jupyter Notebook
74
star
3

SpiceMix

spatial transcriptome, single cell
Jupyter Notebook
62
star
4

SNIPER

nuclear compartments, subcompartments, nuclear organization, Hi-C, autoencoder
Python
29
star
5

MATCHA

multiway chromatin interaction, 3D genome, single-nucleus, hypergraph representation learning
Python
28
star
6

Weaver

Allele-Specific Quantification of Structural Variations in Cancer Genomes
C++
17
star
7

Fast-Higashi

single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, tensor decomposition
Jupyter Notebook
17
star
8

scGHOST

single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, genome subcompartment
Jupyter Notebook
15
star
9

Phylo-HMRF

Python
15
star
10

PEP

Python
14
star
11

SPEID

Python
14
star
12

GAGE-seq

Data processing and analysis workflow for GAGE-seq, a coassay of single-cell HiC and single-cell RNA-seq
Jupyter Notebook
10
star
13

CTCF-MP

Python
9
star
14

UNADON

Transformer-based model to predict genome-wide chromosome spatial position
Python
7
star
15

DANGO

Python
7
star
16

MOCHI

Python
5
star
17

RACA

Perl
5
star
18

MultiRes

Python
4
star
19

MutSpace

cancer mutation, mutation signature, sequence embedding
Python
3
star
20

Phylo-HMGP

Python
3
star
21

DESCHRAMBLER

Perl
2
star
22

ChangeLocator

Python
2
star
23

SPIN

nuclear compartmentalization, 3D genome, nuclear bodies, MRF
Python
2
star
24

MFRT

Shell
1
star
25

Graphene

1
star
26

LDGM

MATLAB
1
star
27

CONCERT

Python
1
star
28

SpaceFormer

Jupyter Notebook
1
star
29

TSA-Seq-toolkit

Python
1
star