Linear Gene Programmes#
💡 Tip: Click the + in the first column to expand detailed method descriptions.
| Method | Year | Task | Model | Published | Code | |
|---|---|---|---|---|---|---|
| AMICI | 2025 | Linear Gene ProgrammesMulti-component Disentanglement |
Linear DecoderCross-attentionSpatially-informed |
✗ | GitHub | |
| CellCap | 2024 | Multi-component DisentanglementLinear Gene Programmes |
VAEAttentionLinear Decoder |
✓ | GitHub | |
| cLVM | 2019 | Linear Gene ProgrammesContrastive Disentanglement |
Factor ModelsContastive VAE |
✓ | GitHub | |
| cPCA | 2018 | Linear Gene ProgrammesContrastive Disentanglement |
Modified PCA |
✓ | GitHub | |
| CPLVMs | 2022 | Linear Gene ProgrammesContrastive Disentanglement |
NB likelihoodFactor Models |
✓ | GitHub | |
| CSMF | 2019 | Linear Gene ProgrammesContrastive Disentanglement |
NMF |
✓ | GitHub | |
| Decipher | 2024 | Unsupervised DisentanglementLinear Gene Programmes |
VAELinear Decoder |
✗ | GitHub | |
| DIALOGUE | 2022 | Linear Gene Programmes |
Sparse CCAPartial CorrelationsMixed Linear Model |
✓ | GitHub | |
| EXPORT | 2024 | Linear Gene Programmes |
VAELinear DecoderPK Representations |
✓ | GitHub | |
| GEDI | 2024 | Linear Gene Programmes |
ProbabilisticSample-specific DecodersPK Representations (optional)RNA Velocity (optional) |
✓ | GitHub | |
| GSFA | 2024 | Multi-component DisentanglementCausal StructureLinear Gene Programmes |
Factor AnalysisProbabilistic |
✓ | GitHub | |
| MEFISTO | 2022 | Linear Gene ProgrammesUnsupervised Disentanglement |
Group Factor ModelMulti-modalSpatially-informedTime-resolved |
✓ | GitHub | |
| Memento | 2024 | Differential AnalysisLinear Gene ProgrammesFeature Relationships |
Hypergeometric testProbabilistic |
✓ | GitHub | |
| Mixscape | 2021 | Perturbation ResponsivenessLinear Gene Programmes |
Gaussian Mixture ModelLDA |
✓ | GitHub | |
| MOFA-FLEX | 2025 | Linear Gene ProgrammesUnsupervised DisentanglementMulti-component Disentanglement |
Group Factor ModelMulti-modalPK RepresentationsSpatially-informedTime-resolvedGaussian Process priorsStochastic Variational Inference |
✗ | GitHub | |
| MOFA+ | 2020 | Linear Gene ProgrammesUnsupervised Disentanglement |
Group Factor ModelMulti-modal |
✓ | GitHub | |
| MOFAcell | 2023 | Linear Gene Programmes |
Group Factor Analysis (MOFA+) |
✓ | GitHub | |
| MUSIC | 2019 | Perturbation ResponsivenessLinear Gene Programmes |
Topic Model |
✓ | GitHub | |
| MuVi | 2023 | Linear Gene ProgrammesUnsupervised Disentanglement |
Group Factor ModelPK RepresentationsMulti-modal |
✓ | GitHub | |
| NicheCompass | 2024 | Linear Gene Programmes |
Graph VAELinear DecoderNB LikelihoodSpatially-informedPK RepresentationsMulti-modal |
✓ | GitHub | |
| ontoVAE | 2023 | Linear Gene Programmes |
VAELinear DecoderPK Representations |
✓ | GitHub | |
| PCPCA | 2024 | Linear Gene ProgrammesContrastive Disentanglement |
modified PCA |
✓ | GitHub | |
| pmVAE | 2021 | Linear Gene Programmes |
Multiple VAEsPK Representations |
✓ | GitHub | |
| scETM | 2021 | Linear Gene Programmes |
VAEEmbedding Topic ModelLinear DecoderPK Representations |
✓ | GitHub | |
| scINSIGHT | 2022 | Contrastive DisentanglementLinear Gene Programmes |
NMF |
✓ | GitHub | |
| scITD | 2024 | Linear Gene Programmes |
Tensor Decomposition (Tucker) |
✓ | GitHub | |
| scPCA | 2020 | Linear Gene ProgrammesContrastive Disentanglement |
Modified PCA |
✓ | GitHub | |
| scRANK | 2024 | Linear Gene ProgrammesPerturbation ResponsivenessGRN Inference |
PC RegressionTensor Decomposition (PARAFAC)Network Diffusion |
✓ | GitHub | |
| Spectra | 2023 | Linear Gene ProgrammesMulti-component Disentanglement |
Poisson LikelihoodFactor AnalysisPK Representations |
✓ | GitHub | |
| STAMP | 2024 | Linear Gene ProgrammesUnsupervised Disentanglement |
Spatially-informedTime-resolvedGraph encoderFactor Analysis |
✓ | GitHub | |
| VEGA | 2023 | Linear Gene Programmes |
VAELinear DecoderPK Representations |
✓ | GitHub | |
| Waddington-OT | 2019 | Trace Cell PopulationsLinear Gene Programmes |
Unbalanced OTEntropy-regularized Sinkhorn |
✓ | GitHub |