14 skills found
kstreet13 / SlingshotFunctions for identifying and characterizing continuous developmental trajectories in single-cell data.
facebookresearch / PoincareMapsThe need to understand cell developmental processes has spawned a plethora of computational methods for discovering hierarchies from scRNAseq data. However, existing techniques are based on Euclidean geometry which is not an optimal choice for modeling complex cell trajectories with multiple branches. To overcome this fundamental representation issue we propose Poincaré maps, a method harnessing the power of hyperbolic geometry into the realm of single-cell data analysis.
farrellja / URDURD - Reconstruction of Branching Developmental Trajectories
pyrovelocity / Pyrovelocity𝒫robabilistic modeling of RNA velocity ⬱
ManuSetty / WishboneWishbone is an algorithm to align cells along developmental trajectories with branches
gioda / FeARLesS4D reconstruction of developmental trajectories using spherical harmonics
sqjin / ScEpathAn energy landscape-based approach for measuring developmental states and inferring cellular trajectories from single cell RNA-seq data
D-score / DscoreD-score for Child Development
gunsagargulati / CytoTRACECytoTRACE (Cellular (Cyto) Trajectory Reconstruction Analysis using gene Counts and Expression) is a computational method that predicts the differentiation state of cells from single-cell RNA-sequencing data. CytoTRACE leverages a simple, yet robust, determinant of developmental potential—the number of detectably expressed genes per cell, or gene counts. We have validated CytoTRACE on ~150K single-cell transcriptomes spanning 315 cell phenotypes, 52 lineages, 14 tissue types, 9 scRNA-seq platforms, and 5 species.
PeterZZQ / VeloSimThis package simulates single cell RNA sequencing data during cell developmental process, the simulation includes unspliced RNA count, spliced RNA count, RNA velocity and cell developmental pseudo-time. The simulation can be used to benchmark computational methods including trajectory inference and RNA velocity inference.
ucasdp / DensityPathA novel algorithm, DensityPath, which accurately and efficiently reconstructs the underlying cell developmental trajectories for large-scale scRNAseq data.
cole-trapnell-lab / ScRNASeqSimA simulator for measuring developmental trajectories with single-cell RNA-seq
Cameron7195 / Math MorphogenesisA model + toolkit for training cellular self-organization and simulating the developmental trajectories of organisms in 3D.
BitaoQiu / Devo AntsKey codes for Towards a developmental biology of superorganisms: reconstructing the canalized trajectories of caste differentiation in ants
