Skip to content
A collection of 50+ trajectory inference methods within a common interface 📥📤
Branch: master
Clone or download
rcannood Merge pull request #154 from dynverse/devel
Implement workaround for h5 1.8.4 on windows; rebuild all containers
Latest commit 9514446 Apr 6, 2019
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
R fix container Apr 6, 2019
data-raw remove trailing commas Apr 5, 2019
data fix container Apr 6, 2019
inst
man fix container Apr 6, 2019
template_container
tests
.Rbuildignore add logs folder to buildignore Oct 15, 2018
.gitignore fix gitignore Sep 3, 2018
.travis.yml dont bother with cache Apr 6, 2019
DESCRIPTION updae readme, description and news Apr 5, 2019
NAMESPACE update dynmethods with new containers Sep 21, 2018
README.Rmd check build status of master branch, not dynwrapv2 Apr 5, 2019
README.md check build status of master branch, not dynwrapv2 Apr 5, 2019
_pkgdown.yml update news for dynwrap v1.0.0 Mar 28, 2019
dynmethods.Rproj add rproj? Jul 2, 2018

README.md

ℹ️ Tutorials     ℹ️ Reference documentation

A collection of 55 trajectory inference methods

This package contains wrappers for trajectory inference (TI) methods. The output of each method is transformed into a common trajectory model using dynwrap, which allows easy visualisation and comparison. All methods are wrapped inside a docker container, which avoids dependency issues, and also makes it easy to add a new method.

To run any of these methods, interpret the results and visualise the trajectory, see the dyno package.

To include your own method, feel free to send us a pull request or create an issue. The easiest way to add a new method is through a docker container, so that dependencies don’t pose any issues for other users, but we also welcome methods directly wrapped inside of R. The main benefit of adding your own method is that users can easily compare your method with others and visualise/interpret the output. Moreover, your method will be compared to other methods within the TI method evaluation.

List of included methods

Method Doi Code Docker Status Authors
Angle code Version Build status
CALISTA code Version Build status Nan Papili Gao
CellRouter code Version Build status Edroaldo Lummertz da Rocha
James J. Collins
George Q. Daley
CellTrails code Version Build status Daniel Ellwanger
cellTree Gibbs code Version Build status David duVerle
Koji Tsuda
cellTree maptpx code Version Build status David duVerle
Koji Tsuda
cellTree vem code Version Build status David duVerle
Koji Tsuda
Component 1 code Version Build status
DPT code Version Build status Laleh Haghverdi
Philipp Angerer
Fabian Theis
ElPiGraph code Version Build status Luca Albergante
ElPiGraph - Cycle code Version Build status Luca Albergante
ElPiGraph - Linear code Version Build status Luca Albergante
Embeddr code Version Build status Kieran Campbell
FateID code Version Build status Dominic Grün
FORKS code Version Build status Mayank Sharma
GNG code Version Build status Robrecht Cannoodt
GPfates code Version Build status Valentine Svensson
Sarah A. Teichmann
GrandPrix code Version Build status Sumon Ahmed
MATCHER code Version Build status Joshua Welch
Jan Prins
MERLoT code Version Build status Gonzalo Parra
Johannes Söding
MFA code Version Build status Kieran Campbell
Christopher Yau
Monocle DDRTree code Version Build status Xiaojie Qiu
Cole Trapnell
Monocle ICA code Version Build status Xiaojie Qiu
Cole Trapnell
Mpath code Version Build status Michael Poidinger
Jinmiao Chen
MST code Version Build status
ouija code Version Build status Kieran Campbell
Christopher Yau
ouijaflow code Version Build status Kieran Campbell
Christopher Yau
PAGA code Version Build status Alexander Wolf
Fabian Theis
PAGA Tree code Version Build status Alexander Wolf
Fabian Theis
pCreode code Version Build status Charles A. Herring
Ken S. Lau
Periodic PrinCurve code Version Build status
PhenoPath code Version Build status Kieran Campbell
Christopher Yau
Projected DPT code Version Build status
Projected Monocle code Version Build status
Projected PAGA code Version Build status
Projected Slingshot code Version Build status
Projected TSCAN code Version Build status
pseudogp code Version Build status Kieran Campbell
Christopher Yau
RaceID / StemID code Version Build status Dominic Grün
Alexander van Oudenaarden
reCAT code Version Build status Riu Jian
SCIMITAR code Version Build status Josh Stuart
SCORPIUS code Version Build status Robrecht Cannoodt
Wouter Saelens
Yvan Saeys
SCOUP code Version Build status Hirotaka Matsumoto
SCUBA code Version Build status Eugenio Marco
Gregory Giecold
Guo-Cheng Yuan
Sincell code Version Build status Antonio Rausell
Miguel Julia
SLICE code Version Build status Yan Xu
Minzhe Guo
SLICER code Version Build status Joshua Welch
Jan Prins
Slingshot code Version Build status Kelly Street
Sandrine Dudoit
STEMNET code Version Build status Lars Velten
topslam code Version Build status Max Zwiessele
TSCAN code Version Build status Zhicheng Ji
Hongkai Ji
URD code Version Build status Jeffrey A. Farrell
Wanderlust code Version Build status Manu Setty
Dana Pe’er
Waterfall code Version Build status Jaehoon Shin
Hongjun Song
Wishbone code Version Build status Manu Setty
Dana Pe’er

Sources

We used following resources to get a (hopefully exhaustive) list of all TI methods:

Anthony Gitter’s single-cell-pseudotime DOI

Sean Davis’ awesome-single-cell DOI

Luke Zappia’s scRNA-tools DOI

New methods

Some methods are not wrapped (yet). Check out the issues for an overview

Latest changes

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

Recent changes in dynmethods 1.0.1

  • FIX: Update version numbers of methods due to workaround for hdf5r on windows.

Recent changes in dynmethods 1.0.0 (28-03-2019)

  • MAJOR CHANGE: Compatibility with dynwrap v1.0.0

  • MAJOR CHANGE: dynmethods package is now coupled to particular tags of dynmethods containers

  • MAJOR CHANGE: The format of the dynmethods::methods object has been changed.

  • MAJOR CHANGE: All methods now work with sparse matrices and dyncli

  • DOCUMENTATION: Improved method documentation

Dynverse dependencies

You can’t perform that action at this time.