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.
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nonnegative-matrix-factorizationsingle-cellopenblascpp
10.62 score 431 stars 2 dependents 498 scripts 1.5k downloadsRcppPlanc - 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>.
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openblashwlochdf5glibccppopenmp
6.92 score 8 stars 3 dependents 31 scripts 1.5k downloadscytosignal - Location and Dynamics of Ligand-Receptor Signaling at Cellular Resolution from Spatial Transcriptomics Data
What the package does (one paragraph).
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openblascpp
4.80 score 30 stars 14 scripts
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:10.1093/bioinformatics/btaf119> for more details.
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openblascpp
4.78 score 6 stars 5 scripts 577 downloads