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Hyper-SAGNN
hypergraph representation learning, graph neural networkHigashi
single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraphSpiceMix
spatial transcriptome, single cellSNIPER
nuclear compartments, subcompartments, nuclear organization, Hi-C, autoencoderMATCHA
multiway chromatin interaction, 3D genome, single-nucleus, hypergraph representation learningWeaver
Allele-Specific Quantification of Structural Variations in Cancer GenomesFast-Higashi
single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, tensor decompositionscGHOST
single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, genome subcompartmentPhylo-HMRF
PEP
SPEID
GAGE-seq
Data processing and analysis workflow for GAGE-seq, a coassay of single-cell HiC and single-cell RNA-seqCTCF-MP
UNADON
Transformer-based model to predict genome-wide chromosome spatial positionDANGO
MOCHI
MultiRes
MutSpace
cancer mutation, mutation signature, sequence embeddingPhylo-HMGP
DESCHRAMBLER
ChangeLocator
SPIN
nuclear compartmentalization, 3D genome, nuclear bodies, MRFMFRT
Graphene
LDGM
CONCERT
SpaceFormer
TSA-Seq-toolkit
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