README.md

ℹ️ Tutorials     ℹ️ Reference documentation

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

Sources

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

Anthony Gitter’s single-cell-pseudotime

Sean Davis’ awesome-single-cell

Luke Zappia’s scRNA-tools

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

Dynverse dependencies