dynverse/dyno

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Created over 6 years ago
Updated over 3 years ago

dynverse/dyno

dynverse

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

ℹ️ Tutorials ℹ️ Reference documentation

Inferring trajectories using dyno

The dyno package offers end-users a complete TI pipeline. It features:

a uniform interface to 60 TI methods,
an interactive guideline tool to help the user select the most appropriate method,
streamlined interpretation and visualisation of trajectories, including colouring by gene expression or clusters, and
downstream analyses such as the identification of potential marker genes.

For information on how to use dyno, check out the installation instructions, tutorials and documentation at dynverse.org

Latest changes

Check out news(package = "dyno") or NEWS.md for a full list of changes.

Recent changes in dyno 0.1.1 (06-04-2019)

BUGFIX: Fixed example dataset
MINOR CHANGE: Bumping version requirement of dynmethods to 1.0.1.

Recent changes in dyno 0.1.0 (29-03-2019)

Initial beta release of dyno

Dynverse dependencies

dynbenchmark

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

dynmethods

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

dynverse

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

dyngen

Simulating single-cell data using gene regulatory networks 📠

anndata

Annotated multivariate observation data in R

dynplot

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

funkyheatmap

Visualising data frames as funky heatmaps 📊

babelwhale

Talking to Docker and Singularity containers

dynguidelines

Selecting the optimal trajectory inference based on a given dataset and user input 🔮

dynwrap

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

dyntoy

Toy synthetic data for testing and prototyping trajectory inference methods 🎲

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

dyneval

Metrics to compare two or more trajectories ⚖

dynutils

Common Functionality for the 'dynverse' Packages

dynparam

competition

Topcoder single-cell trajectory inference competition

travis_scripts

Helper scripts for testing containers on Travis

dyncli

CLI helper package for creating TI containers

ti_paga

funky_cover

ti_monocle_ica

ti_scorpius