scregclust - Reconstructing the Regulatory Programs of Target Genes in scRNA-Seq Data

Implementation of the scregclust algorithm described in Larsson, Held, et al. (2024) <doi:10.1038/s41467-024-53954-3> which reconstructs regulatory programs of target genes in scRNA-seq data. Target genes are clustered into modules and each module is associated with a linear model describing the regulatory program.

Last updated 7 hours ago

clusteringregulatory-programsscrna-seq-analysis

6.09 score 9 stars 25 scripts

CMF - Collective Matrix Factorization

Collective matrix factorization (CMF) finds joint low-rank representations for a collection of matrices with shared row or column entities. This code learns a variational Bayesian approximation for CMF, supporting multiple likelihood potentials and missing data, while identifying both factors shared by multiple matrices and factors private for each matrix. For further details on the method see Klami et al. (2014) <arXiv:1312.5921>. The package can also be used to learn Bayesian canonical correlation analysis (CCA) and group factor analysis (GFA) models, both of which are special cases of CMF. This is likely to be useful for people looking for CCA and GFA solutions supporting missing data and non-Gaussian likelihoods. See Klami et al. (2013) <https://research.cs.aalto.fi/pml/online-papers/klami13a.pdf> and Virtanen et al. (2012) <http://proceedings.mlr.press/v22/virtanen12.html> for details on Bayesian CCA and GFA, respectively.

Last updated 2 years ago

bayesian-inferencecmfdata-integration

3.30 score 1 stars 8 scripts 256 downloads

mmpca - Integrative Analysis of Several Related Data Matrices

A generalization of principal component analysis for integrative analysis. The method finds principal components that describe single matrices or that are common to several matrices. The solutions are sparse. Rank of solutions is automatically selected using cross validation. The method is described in Kallus et al. (2019) <arXiv:1911.04927>.

Last updated 2 years ago

data-integration

3.00 score 2 stars 224 downloads