dynverse: benchmarking, constructing and interpreting single-cell trajectories

dynbenchmark

Comparison of methods for trajectory inference on single-cell data 🥇

dyno

Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕

dynmethods

A collection of 50+ trajectory inference methods within a common interface 📥📤

dyngen

Simulating single-cell data using gene regulatory networks 📠

dynverse

A set of tools supporting the development, execution, and benchmarking of trajectory inference methods. 🌍

anndata

Annotated multivariate observation data in R

dynplot

Visualising single-cell trajectories, including comparisons between two models 📈

babelwhale

Talking to Docker and Singularity containers

dynwrap

A common data format and inference environment for single-cell trajectories 📦

dyndimred

Dimred methods for TI

lmds

Landmark Multi-Dimensional Scaling

dynbenchmark_results

Contains the results from the dynbenchmark evaluation, see https://github.com/dynverse/dynbenchmark

dyngen_manuscript

dynparam

dynutils

Common Functionality for the 'dynverse' Packages

dyncli

CLI helper package for creating TI containers

ti_paga

ti_scorpius

dynplot2

A grammar of graphics for single-cell trajectories 📈

dynfeature

Extracting relevant features from single-cell trajectories 🎯

dynio

dynsite

Generator for the dynverse website at dynverse.github.io

dynverse.github.io

Hub website for the dynverse, pointing visitors towards the different repositories and app

proxyC

R package for large-scale similarity/distance computation

SingleCellOpenProblems

Formalizing and benchmarking open problems in single-cell genomics

ti_cellrouter

ti_forks

ti_monocle3

ti_slingshot

travis_package_cacher

Helper repository to make daily caches of dynverse packages