rliger - Linked Inference of Genomic Experimental Relationships

Uses an extension of nonnegative matrix factorization to identify shared and dataset-specific factors. See Welch J, Kozareva V, et al (2019) <doi:10.1016/j.cell.2019.05.006>, and Liu J, Gao C, Sodicoff J, et al (2020) <doi:10.1038/s41596-020-0391-8> for more details.

Last updated 5 months ago

nonnegative-matrix-factorizationsingle-cell

380 stars 6.80 score 78 dependencies 1 dependents

RcppPlanc - Parallel Low-Rank Approximation with Nonnegativity Constraints

'Rcpp' bindings for 'PLANC', a highly parallel and extensible NMF/NTF (Non-negative Matrix/Tensor Factorization) library. Wraps algorithms described in Kannan et. al (2018) <doi:10.1109/TKDE.2017.2767592> and Eswar et. al (2021) <doi:10.1145/3432185>. Implements algorithms described in Welch et al. (2019) <doi:10.1016/j.cell.2019.05.006>, Gao et al. (2021) <doi:10.1038/s41587-021-00867-x>, and Kriebel & Welch (2022) <doi:10.1038/s41467-022-28431-4>.

Last updated 11 days ago

3 stars 2.53 score 5 dependencies

cytosignal - What the Package Does (One Line, Title Case)

What the package does (one paragraph).

Last updated 2 months ago

12 stars 2.22 score 44 dependencies

CytoSimplex - Simplex Visualization of Cell Fate Similarity in Single-Cell Data

Create simplex plots to visualize the similarity between single-cells and selected clusters in a 1-/2-/3-simplex space. Velocity information can be added as an additional layer. See Liu J, Wang Y et al (2023) <doi:10.1101/2023.12.07.570655> for more details.

Last updated 4 months ago

1 stars 1.33 score 75 dependencies

SiNMFiD - Supervised iNMF informed Deconvolution

A package for completing cell type deconvolution on bulk spatial transcriptomic data utilizing multiple reference scRNA-seq datasets.

Last updated 6 months ago

0.91 score 107 dependencies