slingshot

Trajectory analyzer

An R package and Python implementation for analyzing developmental trajectories in single-cell RNA sequencing data

Functions for identifying and characterizing continuous developmental trajectories in single-cell data.

GitHub

275 stars
8 watching
43 forks
Language: R
last commit: over 2 years ago
Linked from 1 awesome list


Backlinks from these awesome lists:

Related projects:

RepositoryDescriptionStars
theislab/kbranchesA software package to identify regions of interest in single-cell differentiation trajectories5
phoenixding/scdiffAnalyzes single-cell RNA-seq data to predict cell differentiation trajectories and associated transcription factors and genes.28
jw156605/slicerAn R package implementing an algorithm for inferring cell trajectories based on gene expression data12
kchen-lab/cyclumA tool to identify circular trajectories in scRNA-seq data using an autoencoder with sinusoidal activations20
mdtraj/mdtrajAn open-source library for analyzing molecular dynamics trajectories602
dynverse/dynverseSupports the development and benchmarking of trajectory inference methods in single-cell biology72
kstreet13/bioc2020trajectoriesAnalyzing and comparing single-cell RNA-seq data across multiple conditions to infer cell trajectories and detect differential expression.25
dimenwarper/scimitarAnalyzes single-cell measurements to infer morphing trajectories and their associated regulation.7
d-seams/seams-coreAnalyzes molecular dynamics trajectories to infer structural properties of molecules35
snakemake-workflows/single-cell-rna-seqA workflow generator for single-cell RNA-seq data analysis100
rabadanlab/sctdaAn object-oriented Python library for analyzing single-cell RNA-seq data using topological representations7
thomas-haslwanter/scikit-kinematicsA set of Python functions and classes for analyzing 3D kinematics data from various sensors.131
thomasjkeel/jsmetricsA Python package providing algorithms and metrics to analyze atmospheric jet streams25
nasqar/seuratv3wizardAn R-based web application for guided single-cell RNA-seq data analysis and clustering33
roboticexplorationlab/trajectoryoptimization.jlA package that provides an efficient API and methods for defining and evaluating trajectory optimization problems in Julia.343