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

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# A collection of 56 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
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
FORKS code Version Build status Mayank Sharma
FateID code Version Build status Dominic Grün
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
MST code Version Build status
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
Oscope code Version Build status Ning Leng
PAGA code Version Build status Alexander Wolf
Fabian Theis
PAGA Tree code Version Build status Alexander Wolf
Fabian Theis
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
RaceID / StemID code Version Build status Dominic Grün
Alexander van Oudenaarden
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
SLICE code Version Build status Yan Xu
Minzhe Guo
SLICER code Version Build status Joshua Welch
Jan Prins
STEMNET code Version Build status Lars Velten
Sincell code Version Build status Antonio Rausell
Miguel Julia
Slingshot code Version Build status Kelly Street
Sandrine Dudoit
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
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
ouija code Version Build status Kieran Campbell
Christopher Yau
ouijaflow code Version Build status Kieran Campbell
Christopher Yau
pCreode code Version Build status Charles A. Herring
Ken S. Lau
pseudogp code Version Build status Kieran Campbell
Christopher Yau
reCAT code Version Build status Riu Jian
topslam code Version Build status Max Zwiessele

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 1.1.0 (unreleased)

  • MAJOR CHANGE: Add functionality to switch between R wrappers and container wrappers.

  • MAJOR CHANGE: Add R wrappers for SCORPIUS.

  • BUG FIX: Do not install R packages if version is not specified and package is installed.

Recent changes in dynmethods 1.0.5 (03-07-2019)

  • SMALL CHANGES: Updates for scorpius, slingshot, paga, paga_tree and paga_projected

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